1 TODO
1.1 202511
- We have some samples which are defined as persistent via 7SL. Can we see some reads in those samples?
- Send file with mapped reads per sample for all human samples.
- Queue SL read counter for all human samples.
- All samples have nasal, skin, PBMC; all patients are nasal + or nasal -; perform contrasts of nasal+/nasal- of the PBMC samples. For the PBMC samples, recast them as +/-
1.2 202601
- 7SL positive vs negative for
- Add plot of transcriptome clustering of nasal swabs between nasal positive/negative with the caveat that the are only 2 positives, 8 negatives, and 1 undetermined in the stranded library; the ribozero have 5 positive, 3 negative, and 1 undetermined.
- Create a relative abundance of bacteria/viruses observed in the nassal samples; counting at genus.
Note that this requires splitting the data into 4 groups: salmon+rz, salmon+mrna, hisat+rz, hisat+mrna.
2 Changelog
2.1 202511
Following my conversation with Maria Adelaida, I downloaded a new copy of our online sample sheet and made a sub-copy with only the human samples. It is named (creatively) sample_sheets/human_samples_202511.xlsx
3 Introduction
I want to use this document to examine our first round of persistence samples. I checked my email from Najib and did not find a sample sheet but did find an explanation of the three sample types we expect.
In preparation for this, I downloaded a new hg38 genome. Since the panamensis asembly has not significantly changed (excepting the putative long read genome which I have not yet seen), I am just using the same one.
4 Loading annotation
The hg38 genome I got is brand new (202405), so do not use the archive for a while.
## Ok, so useast.ensembl is failing today, let us use the jan2024 archive?
#hs_annot <- load_biomart_annotations(archive = FALSE, species = "hsapiens")
## Seems like the 202401 archive is a good choice, it is explicitly the hg38_111 release.
## and it is waaaaay faster (like 100x) than useast right now.
hs_annot <- load_biomart_annotations(archive = FALSE, species = "hsapiens", overwrite = TRUE,
year = 2025, month = "08")## Using mart: ENSEMBL_MART_ENSEMBL from host: useast.ensembl.org.## Successfully connected to the hsapiens_gene_ensembl database.## Finished downloading ensembl gene annotations.## Finished downloading ensembl structure annotations.## symbol columns is null, pattern matching 'symbol' and taking the first.## Found 2 potential symbol columns, using the first:hgnc_symbol.## Including symbols, there are 86371 vs the 533740 gene annotations.## Not dropping haplotype chromosome annotations, set drop_haplotypes = TRUE if this is bad.## Saving annotations to hsapiens_biomart_annotations.rda.## Finished save().panamensis_orgdb_idx <- grep(pattern = "^org.+panamen.+MHOM.+db$", x = rownames(installed.packages()))
panamensis_orgdb <- tail(rownames(installed.packages())[panamensis_orgdb_idx], n = 1)
lp_annot <- load_orgdb_annotations(panamensis_orgdb, keytype = "gid")## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:hpgltools':
##
## annotation<-, conditions, conditions<-## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
##
## anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter,
## Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit,
## which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
## and for packages 'citation("pkgname")'.##
## Attaching package: 'Biobase'## The following object is masked from 'package:hpgltools':
##
## notes## Loading required package: IRanges## Loading required package: S4Vectors##
## Attaching package: 'S4Vectors'## The following object is masked from 'package:utils':
##
## findMatches## The following objects are masked from 'package:base':
##
## expand.grid, I, unname##
## Attaching package: 'IRanges'## The following object is masked from 'package:hpgltools':
##
## trim## ## Unable to find CDSNAME, setting it to ANNOT_EXTERNAL_DB_NAME.## Unable to find CDSCHROM in the db, removing it.## Unable to find CDSSTRAND in the db, removing it.## Unable to find CDSSTART in the db, removing it.## Unable to find CDSEND in the db, removing it.## Extracted all gene ids.## Attempting to select: ANNOT_EXTERNAL_DB_NAME, GENE_TYPE## 'select()' returned 1:1 mapping between keys and columnsThis is a little silly, but I am going to reload the annotations using the previous invocation to extract the annotation table without having to think. The previous block loads the orgdb for me, so I can just use that to get the fun annotations.
## Unable to find CDSNAME, setting it to ANNOT_EXTERNAL_DB_NAME.## Unable to find CDSCHROM in the db, removing it.## Unable to find CDSSTRAND in the db, removing it.## Unable to find CDSSTART in the db, removing it.## Unable to find CDSEND in the db, removing it.## Extracted all gene ids.## Attempting to select: ANNOT_EXTERNAL_DB_NAME, GENE_TYPE, ANNOT_AA_SEQUENCE_ID, ANNOT_ANNOTATED_GO_COMPONENT, ANNOT_ANNOTATED_GO_FUNCTION, ANNOT_ANNOTATED_GO_ID_COMPONENT, ANNOT_ANNOTATED_GO_ID_FUNCTION, ANNOT_ANNOTATED_GO_ID_PROCESS, ANNOT_ANNOTATED_GO_PROCESS, ANNOT_ANTICODON, ANNOT_APOLLO_LINK_OUT, ANNOT_APOLLO_TRANSCRIPT_DESCRIPTION, ANNOT_CDS, ANNOT_CDS_LENGTH, ANNOT_CHROMOSOME, ANNOT_CODING_END, ANNOT_CODING_START, ANNOT_EC_NUMBERS, ANNOT_EC_NUMBERS_DERIVED, ANNOT_END_MAX, ANNOT_EXON_COUNT, ANNOT_EXTERNAL_DB_NAME, ANNOT_EXTERNAL_DB_VERSION, ANNOT_FIVE_PRIME_UTR_LENGTH, ANNOT_GENE_CONTEXT_END, ANNOT_GENE_CONTEXT_START, ANNOT_GENE_END_MAX, ANNOT_GENE_END_MAX_TEXT, ANNOT_GENE_ENTREZ_ID, ANNOT_GENE_ENTREZ_LINK, ANNOT_GENE_EXON_COUNT, ANNOT_GENE_HTS_NONCODING_SNPS, ANNOT_GENE_HTS_NONSYN_SYN_RATIO, ANNOT_GENE_HTS_NONSYNONYMOUS_SNPS, ANNOT_GENE_HTS_STOP_CODON_SNPS, ANNOT_GENE_HTS_SYNONYMOUS_SNPS, ANNOT_GENE_LOCATION_TEXT, ANNOT_GENE_NAME, ANNOT_GENE_ORTHOLOG_NUMBER, ANNOT_GENE_ORTHOMCL_NAME, ANNOT_GENE_PARALOG_NUMBER, ANNOT_GENE_PREVIOUS_IDS, ANNOT_GENE_PRODUCT, ANNOT_GENE_START_MIN, ANNOT_GENE_START_MIN_TEXT, ANNOT_GENE_TOTAL_HTS_SNPS, ANNOT_GENE_TRANSCRIPT_COUNT, ANNOT_GENE_TYPE, ANNOT_GENOMIC_SEQUENCE_LENGTH, ANNOT_GENUS_SPECIES, ANNOT_HAS_MISSING_TRANSCRIPTS, ANNOT_INTERPRO_DESCRIPTION, ANNOT_INTERPRO_ID, ANNOT_IS_DEPRECATED, ANNOT_IS_PSEUDO, ANNOT_ISOELECTRIC_POINT, ANNOT_LOCATION_TEXT, ANNOT_MAP_LOCATION, ANNOT_MCMC_LOCATION, ANNOT_MOLECULAR_WEIGHT, ANNOT_NCBI_TAX_ID, ANNOT_ORTHOMCL_LINK, ANNOT_OVERVIEW, ANNOT_PFAM_DESCRIPTION, ANNOT_PFAM_ID, ANNOT_PIRSF_DESCRIPTION, ANNOT_PIRSF_ID, ANNOT_PREDICTED_GO_COMPONENT, ANNOT_PREDICTED_GO_FUNCTION, ANNOT_PREDICTED_GO_ID_COMPONENT, ANNOT_PREDICTED_GO_ID_FUNCTION, ANNOT_PREDICTED_GO_ID_PROCESS, ANNOT_PREDICTED_GO_PROCESS, ANNOT_PRIMARY_KEY, ANNOT_PROB_MAP, ANNOT_PROB_MCMC, ANNOT_PROSITEPROFILES_DESCRIPTION, ANNOT_PROSITEPROFILES_ID, ANNOT_PROTEIN_LENGTH, ANNOT_PROTEIN_SEQUENCE, ANNOT_PROTEIN_SOURCE_ID, ANNOT_PSEUDO_STRING, ANNOT_SEQUENCE_DATABASE_NAME, ANNOT_SEQUENCE_ID, ANNOT_SIGNALP_PEPTIDE, ANNOT_SMART_DESCRIPTION, ANNOT_SMART_ID, ANNOT_SNPOVERVIEW, ANNOT_SO_ID, ANNOT_SO_TERM_DEFINITION, ANNOT_SO_TERM_NAME, ANNOT_SO_VERSION, ANNOT_START_MIN, ANNOT_STRAND, ANNOT_STRAND_PLUS_MINUS, ANNOT_SUPERFAMILY_DESCRIPTION, ANNOT_SUPERFAMILY_ID, ANNOT_THREE_PRIME_UTR_LENGTH, ANNOT_TIGRFAM_DESCRIPTION, ANNOT_TIGRFAM_ID, ANNOT_TM_COUNT, ANNOT_TRANS_FOUND_PER_GENE_INTERNAL, ANNOT_TRANSCRIPT_INDEX_PER_GENE, ANNOT_TRANSCRIPT_LENGTH, ANNOT_TRANSCRIPT_LINK, ANNOT_TRANSCRIPT_PRODUCT, ANNOT_TRANSCRIPT_SEQUENCE, ANNOT_TRANSCRIPTS_FOUND_PER_GENE, ANNOT_UNIPROT_IDS, ANNOT_UNIPROT_LINKS## 'select()' returned 1:1 mapping between keys and columns5 Collect preprocessed metadata
Use my new sample sheet here.
current_samplesheet <- "sample_sheets/human_samples_202511.xlsx"
first_spec <- make_rnaseq_spec()
input <- read_metadata(current_samplesheet)
colnames(input)## [1] "seq" "hpgl_identifier" "aim"
## [4] "participant_code" "sample_type" "tube_label_origin"
## [7] "number_of_vials" "sample_collection_date" "exp_person"
## [10] "clinical_presentation" "parasite" "prior_host_hpgl_code"
## [13] "prior_parasite_hpgl_code" "initial_recurrent" "drug_susceptibility_perc_reduction_gluc"
## [16] "drug_susceptibility_perc_reduction_mlf" "zymodeme_by_electrophoresis" "zymodeme_by_pca"
## [19] "rna_extraction_date" "rna_volume_ul" "rna_qc_date"
## [22] "rna_nanodrop_ng_ul" "X260_280_ratio" "X260_230_ratio"
## [25] "rna_bioanalyzer_or_qubit_ng_ul" "rin" "rna_qc_passed"
## [28] "library_type" "library_version" "library_name"
## [31] "library_const_date" "rna_used_to_construct_libraries_ul" "rna_used_to_construct_libraries_ng"
## [34] "library_qc_date" "lib_qc_passed" "library_volume_ul"
## [37] "unique_dual_index_set" "unique_dual_index_plate_coordinate" "unique_dual_index_id"
## [40] "concentrations_determined_by_1" "primer_conc_ng_ul_30100bp_region_1" "adapter_dimer_conc_ng_ul_100200bp_region_1"
## [43] "library_conc_ng_ul_2001000bp_region_1" "library_molarity_nm_2001000bp_region_1" "library_ave_frag_size_bp_2001000bp_region_1"
## [46] "calculated_adapter_dimer_percent_1" "concentrations_determined_by_2" "primer_conc_ng_ul_30100bp_region_2"
## [49] "adapter_dimer_conc_ng_ul_100200bp_region_2" "library_conc_ng_ul_2001000bp_region_2" "library_molarity_nm_2001000bp_region_2"
## [52] "library_ave_frag_size_bp_2001000bp_region_2" "calculated_adapter_dimer_percent_2" "library_volume_ul_sent_to_umd"
## [55] "shipment_date" "bbiagtc_date_received" "bbiagtc_library_cleanup"
## [58] "bbiagtc_date_sequenced" "bbiagtc_sequence_batch" "bbiagtc_pe_reads_pf"
## [61] "bbiagtc_fastp_duplication_rate" "hisat2inputreads" "lpsingleconaligned"
## [64] "hg38singleconaligned" "lpmulticonaligned" "hg38multiconaligned"
## [67] "lpsingleallaligned" "hg38singleallaligned" "lpmultiallaligned"
## [70] "hg38multiallaligned" "lppercentmappedfromlog" "hg38percentmappedfromlog"
## [73] "lphisatobservedcds" "hg38hisatobservedcds" "krakenmatrix"
## [76] "lphisatgenematrix" "hg38hisatgenematrix" "lpsalmontranscriptmatrix"
## [79] "hg38salmontranscriptmatrix" "detectionparasiteby7sl" "detectionparasiteby18s"
## [82] "detectionparasitebykdnasec" "metabolomicnasalswaborplasma" "immunophenotypingnasalswaborpbmcs"pre_meta <- gather_preprocessing_metadata(
starting_metadata = current_samplesheet, id_column = "hpgl_identifier",
specification = first_spec, new_metadata = "persistence_hu_modified.xlsx",
basedir = "preprocessing", species = c("hg38_115", "lpanamensis_mhomcol_v68"))## Dropped 1 rows from the sample metadata because the sample ID is blank.## Did not find the condition column in the sample sheet.## Filling it in as undefined.## Did not find the batch column in the sample sheet.## Filling it in as undefined.## Checking the state of the condition column.## Checking the state of the batch column.## Checking the condition factor.## Warning in dispatch_regex_search(meta, search, replace, input_file_spec, : NAs introduced by coercion
## Warning in dispatch_regex_search(meta, search, replace, input_file_spec, : NAs introduced by coercion## Writing new metadata to: persistence_hu_modified.xlsx## Deleting the file persistence_hu_modified.xlsx before writing the tables.modified_meta <- pre_meta[["new_meta"]]
## Added the following line to gather_preprocessing_metadata()
rownames(modified_meta) <- make.names(modified_meta[["hpgl_identifier"]], unique = TRUE)
## FIXME: 202511: I broke something in some of these functions and it is pulling
## the wrong information for number of observed genes.
head(modified_meta)## seq hpgl_identifier aim participant_code sample_type tube_label_origin number_of_vials sample_collection_date exp_person
## PRHU0001 1 PRHU0001 aim1 PP1006 PBMCs PP1006 PBMCs 1 2024-01-29 LG
## PRHU0002 2 PRHU0002 aim1 PP2001 nasal swab PP2001 HN 1 2024-02-05 LG
## PRHU0009 4 PRHU0009 aim1 PP2003 PBMCs PP2003 PBMCs 1 <NA> LG
## PRHU0010 5 PRHU0010 aim1 PP2004 PBMCs PP2004 PBMCs 1 2024-04-05 LG
## PRHU0011 6 PRHU0011 aim1 PP2005 PBMCs PP2005 PBMCs 1 2024-04-12 LG
## PRHU0018 7 PRHU0018 aim1 PP2003 WBCs PP2003 WBCs 1 2024-03-22 LG
## clinical_presentation prior_host_hpgl_code rna_extraction_date rna_volume_ul rna_qc_date rna_nanodrop_ng_ul X260_280_ratio
## PRHU0001 HD <NA> 2024-01-31 25 2024-02-15 338.43 2.04
## PRHU0002 HD <NA> 2024-02-14 25 2024-02-15 84.82 2.08
## PRHU0009 H-CL TMRC30130; TMRC30124; TMRC30131 2024-05-06 25 2024-05-06 115.1 1.99
## PRHU0010 H-CL <NA> 2024-05-06 25 2024-05-06 185.28 2.03
## PRHU0011 H-CL <NA> 2024-05-06 25 2024-05-06 70.12 1.95
## PRHU0018 H-CL TMRC30130; TMRC30124; TMRC30131 2024-03-22 30 2024-05-02 49.55 2.06
## X260_230_ratio rna_bioanalyzer_or_qubit_ng_ul rin rna_qc_passed library_type library_version library_name
## PRHU0001 1.73 407 NA yes mRNA 1 PP1006.PBMCs.mRNA.1
## PRHU0002 1.97 101 NA yes mRNA 1 PP2001.nasal swab.mRNA.1
## PRHU0009 1.34 167 8.0 yes mRNA 1 PP2003.PBMCs.mRNA.1
## PRHU0010 1.91 264 8.5 yes mRNA 1 PP2004.PBMCs.mRNA.1
## PRHU0011 0.85 113 8.7 yes mRNA 1 PP2005.PBMCs.mRNA.1
## PRHU0018 1.56 70 9.1 yes mRNA 1 PP2003.WBCs.mRNA.1
## library_const_date rna_used_to_construct_libraries_ul rna_used_to_construct_libraries_ng library_qc_date lib_qc_passed
## PRHU0001 2024-02-09 1.48 500 2024-02-12 yes
## PRHU0002 2024-02-15 3.54 300 2024-02-16 yes
## PRHU0009 2024-06-05 1.79 300 2024-06-11 yes
## PRHU0010 2024-06-05 1.14 300 2024-06-11 yes
## PRHU0011 2024-06-05 2.65 300 2024-06-11 yes
## PRHU0018 2024-06-05 4.29 300 2024-06-11 yes
## library_volume_ul unique_dual_index_set unique_dual_index_plate_coordinate unique_dual_index_id
## PRHU0001 15 IDT for Illumina RNA UD Indexes Set A C04 UDP0027
## PRHU0002 15 IDT for Illumina RNA UD Indexes Set A F04 UDP0030
## PRHU0009 15 IDT for Illumina RNA UD Indexes Set A B05 UDP0034
## PRHU0010 15 IDT for Illumina RNA UD Indexes Set A C05 UDP0035
## PRHU0011 15 IDT for Illumina RNA UD Indexes Set A D05 UDP0036
## PRHU0018 15 IDT for Illumina RNA UD Indexes Set A E05 UDP0037
## concentrations_determined_by_1 primer_conc_ng_ul_30100bp_region_1 adapter_dimer_conc_ng_ul_100200bp_region_1
## PRHU0001 TapeStation - -
## PRHU0002 TapeStation - -
## PRHU0009 Bioanalyzer 0.49 0.27
## PRHU0010 Bioanalyzer 0.58 0.35
## PRHU0011 Bioanalyzer 0.7 0.27
## PRHU0018 Bioanalyzer 0.58 0.12
## library_conc_ng_ul_2001000bp_region_1 library_molarity_nm_2001000bp_region_1 library_ave_frag_size_bp_2001000bp_region_1
## PRHU0001 69.50 321.0 353
## PRHU0002 17.50 82.3 345
## PRHU0009 60.64 293.3 336
## PRHU0010 64.84 314.0 340
## PRHU0011 56.86 279.9 330
## PRHU0018 85.33 421.9 328
## calculated_adapter_dimer_percent_1 concentrations_determined_by_2 primer_conc_ng_ul_30100bp_region_2
## PRHU0001 0 <NA> <NA>
## PRHU0002 0 <NA> <NA>
## PRHU0009 0.00445250659630607 <NA> <NA>
## PRHU0010 0.0053979025293029 <NA> <NA>
## PRHU0011 0.00474850510024622 <NA> <NA>
## PRHU0018 0.00140630493378648 <NA> <NA>
## adapter_dimer_conc_ng_ul_100200bp_region_2 library_conc_ng_ul_2001000bp_region_2 library_molarity_nm_2001000bp_region_2
## PRHU0001 <NA> NA NA
## PRHU0002 <NA> NA NA
## PRHU0009 <NA> NA NA
## PRHU0010 <NA> NA NA
## PRHU0011 <NA> NA NA
## PRHU0018 <NA> NA NA
## library_ave_frag_size_bp_2001000bp_region_2 calculated_adapter_dimer_percent_2 library_volume_ul_sent_to_umd shipment_date
## PRHU0001 NA NA 14 2024-02-20
## PRHU0002 NA NA 14 2024-02-20
## PRHU0009 NA NA 14 2024-08-26
## PRHU0010 NA NA 14 2024-08-26
## PRHU0011 NA NA 14 2024-08-26
## PRHU0018 NA NA 14 2024-08-26
## bbiagtc_date_received bbiagtc_library_cleanup bbiagtc_date_sequenced bbiagtc_sequence_batch bbiagtc_pe_reads_pf
## PRHU0001 2024-04-05 not needed 2024-05-03 PERS001 13167287
## PRHU0002 2024-04-05 not needed 2024-05-03 PERS001 9815642
## PRHU0009 2024-11-05 not needed 2024-11-08 PERS002 23614271
## PRHU0010 2024-11-05 yes 2024-11-08 PERS002 22777166
## PRHU0011 2024-11-05 not needed 2024-11-08 PERS002 23458700
## PRHU0018 2024-11-05 not needed 2024-11-08 PERS002 20907177
## bbiagtc_fastp_duplication_rate detectionparasiteby7sl detectionparasiteby18s detectionparasitebykdnasec metabolomicnasalswaborplasma
## PRHU0001 13.9 <NA> <NA> <NA> <NA>
## PRHU0002 18.4 <NA> <NA> <NA> <NA>
## PRHU0009 19.9 <NA> <NA> <NA> yes
## PRHU0010 16.9 <NA> <NA> <NA> yes
## PRHU0011 20.4 <NA> <NA> <NA> yes
## PRHU0018 16.6 positive positive <NA> yes
## immunophenotypingnasalswaborpbmcs condition batch sampleid trimomatic_input trimomatic_output trimomatic_percent fastqc_pct_gc
## PRHU0001 <NA> undefined undefined PRHU0001 13167287 12085247 0.918 49
## PRHU0002 <NA> undefined undefined PRHU0002 NA NA NA 50
## PRHU0009 <NA> undefined undefined PRHU0009 23614271 22272928 0.943 51
## PRHU0010 <NA> undefined undefined PRHU0010 22777166 21621102 0.949 51
## PRHU0011 <NA> undefined undefined PRHU0011 23458700 22252717 0.949 51
## PRHU0018 <NA> undefined undefined PRHU0018 20907177 19815284 0.948 52
## kraken_bacterial_classified kraken_bacterial_unclassified kraken_first_bacterial_species kraken_first_bacterial_species_reads
## PRHU0001 418110 11667137 Staphylococcus aureus 117628
## PRHU0002 324998 8681618 Bacillus thuringiensis 48125
## PRHU0009 86840 866454 Porphyrobacter sp. GA68 11937
## PRHU0010 76438 1056370 Klebsiella pneumoniae 7070
## PRHU0011 70332 803596 Klebsiella pneumoniae 6002
## PRHU0018 46603 619808 Priestia megaterium 7831
## kraken_viral_classified kraken_viral_unclassified kraken_first_viral_species kraken_first_viral_species_reads
## PRHU0001 58135 12027112 Proteus virus Isfahan 35851
## PRHU0002 43789 8962827 Proteus virus Isfahan 28527
## PRHU0009 197113 22075815 Proteus virus Isfahan 146195
## PRHU0010 132560 21488542 Proteus virus Isfahan 90884
## PRHU0011 204047 22048670 Proteus virus Isfahan 160954
## PRHU0018 108172 19707112 Proteus virus Isfahan 74208
## kraken_matrix_viral
## PRHU0001 preprocessing/PRHU0001/outputs/20250918kraken_viral/kraken_report_matrix.tsv
## PRHU0002 preprocessing/PRHU0002/outputs/20250918kraken_viral/kraken_report_matrix.tsv
## PRHU0009 preprocessing/PRHU0009/outputs/20250918kraken_viral/kraken_report_matrix.tsv
## PRHU0010 preprocessing/PRHU0010/outputs/20250918kraken_viral/kraken_report_matrix.tsv
## PRHU0011 preprocessing/PRHU0011/outputs/20250918kraken_viral/kraken_report_matrix.tsv
## PRHU0018 preprocessing/PRHU0018/outputs/20250918kraken_viral/kraken_report_matrix.tsv
## kraken_matrix_bacterial hisat_rrna_input_reads_hg38_115
## PRHU0001 preprocessing/PRHU0001/outputs/02kraken_bacteria/kraken_report_matrix.tsv 12085247
## PRHU0002 preprocessing/PRHU0002/outputs/02kraken_bacteria/kraken_report_matrix.tsv 9006616
## PRHU0009 preprocessing/PRHU0009/outputs/06kraken_bacteria/kraken_report_matrix.tsv 22272928
## PRHU0010 preprocessing/PRHU0010/outputs/06kraken_bacteria/kraken_report_matrix.tsv 21621102
## PRHU0011 preprocessing/PRHU0011/outputs/06kraken_bacteria/kraken_report_matrix.tsv 22252717
## PRHU0018 preprocessing/PRHU0018/outputs/06kraken_bacteria/kraken_report_matrix.tsv 19815284
## hisat_rrna_input_reads_lpanamensis_mhomcol_v68 hisat_rrna_single_concordant_hg38_115
## PRHU0001 NA 73426
## PRHU0002 NA 80682
## PRHU0009 NA 408744
## PRHU0010 NA 149371
## PRHU0011 NA 200482
## PRHU0018 NA 117268
## hisat_rrna_single_concordant_lpanamensis_mhomcol_v68 hisat_rrna_multi_concordant_hg38_115
## PRHU0001 NA 0
## PRHU0002 NA 3
## PRHU0009 NA 40
## PRHU0010 NA 6
## PRHU0011 NA 1
## PRHU0018 NA 3
## hisat_rrna_multi_concordant_lpanamensis_mhomcol_v68 hisat_rrna_percent_log_hg38_115 hisat_rrna_percent_log_lpanamensis_mhomcol_v68
## PRHU0001 NA 0.63 NA
## PRHU0002 NA 0.94 NA
## PRHU0009 NA 1.93 NA
## PRHU0010 NA 0.73 NA
## PRHU0011 NA 0.94 NA
## PRHU0018 NA 0.62 NA
## hisat_genome_input_reads_hg38_115 hisat_genome_input_reads_lpanamensis_mhomcol_v68 hisat_genome_single_concordant_hg38_115
## PRHU0001 12085247 12085247 11027565
## PRHU0002 9006616 9006616 8119315
## PRHU0009 22272928 22272928 19763135
## PRHU0010 21621102 21621102 19276929
## PRHU0011 22252717 22252717 19973324
## PRHU0018 19815284 19815284 18103721
## hisat_genome_single_concordant_lpanamensis_mhomcol_v68 hisat_genome_multi_concordant_hg38_115
## PRHU0001 838 621289
## PRHU0002 760 505363
## PRHU0009 1382 1516414
## PRHU0010 559 1171082
## PRHU0011 662 1356659
## PRHU0018 415 1010925
## hisat_genome_multi_concordant_lpanamensis_mhomcol_v68 hisat_genome_single_all_hg38_115
## PRHU0001 99 365382
## PRHU0002 102 282669
## PRHU0009 102 790119
## PRHU0010 96 920497
## PRHU0011 82 758139
## PRHU0018 62 536623
## hisat_genome_single_all_lpanamensis_mhomcol_v68 hisat_genome_multi_all_hg38_115 hisat_genome_multi_all_lpanamensis_mhomcol_v68
## PRHU0001 14329 84362 6702
## PRHU0002 13432 71982 7507
## PRHU0009 22507 235198 17740
## PRHU0010 10941 242320 12474
## PRHU0011 12590 206128 13330
## PRHU0018 8241 133869 9468
## hisat_unmapped_hg38_115 hisat_unmapped_lpanamensis_mhomcol_v68 hisat_genome_percent_log_hg38_115
## PRHU0001 36996 24147571 99.85
## PRHU0002 131347 17990551 99.27
## PRHU0009 220613 44502561 99.50
## PRHU0010 189403 43217431 99.56
## PRHU0011 233569 44477964 99.48
## PRHU0018 177472 39611887 99.55
## hisat_genome_percent_log_lpanamensis_mhomcol_v68 hisat_alignment_hg38_115
## PRHU0001 0.09 preprocessing/PRHU0001/outputs/20250918hisat_hg38_115/hg38_115_genome.bam
## PRHU0002 0.13 preprocessing/PRHU0002/outputs/20250918hisat_hg38_115/hg38_115_genome.bam
## PRHU0009 0.10 preprocessing/PRHU0009/outputs/20250918hisat_hg38_115/hg38_115_genome.bam
## PRHU0010 0.06 preprocessing/PRHU0010/outputs/20250918hisat_hg38_115/hg38_115_genome.bam
## PRHU0011 0.06 preprocessing/PRHU0011/outputs/20250918hisat_hg38_115/hg38_115_genome.bam
## PRHU0018 0.05 preprocessing/PRHU0018/outputs/20250918hisat_hg38_115/hg38_115_genome.bam
## hisat_alignment_lpanamensis_mhomcol_v68 salmon_mapped_hg38_115
## PRHU0001 preprocessing/PRHU0001/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome.bam NA
## PRHU0002 preprocessing/PRHU0002/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome.bam NA
## PRHU0009 preprocessing/PRHU0009/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome.bam NA
## PRHU0010 preprocessing/PRHU0010/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome.bam NA
## PRHU0011 preprocessing/PRHU0011/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome.bam NA
## PRHU0018 preprocessing/PRHU0018/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome.bam NA
## salmon_mapped_lpanamensis_mhomcol_v68 salmon_percent_hg38_115 salmon_percent_lpanamensis_mhomcol_v68 salmon_observed_genes_hg38_115
## PRHU0001 228 54.62 0.001887 40892
## PRHU0002 NA 61.09 0.023971 37639
## PRHU0009 514 53.76 0.002308 47176
## PRHU0010 532 55.29 0.002461 47162
## PRHU0011 564 56.48 0.002535 46983
## PRHU0018 411 57.38 0.002074 43731
## salmon_observed_genes_lpanamensis_mhomcol_v68 input_r1 input_r2
## PRHU0001 12 unprocessed/PRHU0001_S49_R1_001.fastq.gz unprocessed/PRHU0001_S49_R2_001.fastq.gz
## PRHU0002 12
## PRHU0009 14 unprocessed/PRHU0009_S7_R1_001.fastq.gz unprocessed/PRHU0009_S7_R2_001.fastq.gz
## PRHU0010 13 unprocessed/PRHU0010_S8_R1_001.fastq.gz unprocessed/PRHU0010_S8_R2_001.fastq.gz
## PRHU0011 15 unprocessed/PRHU0011_S9_R1_001.fastq.gz unprocessed/PRHU0011_S9_R2_001.fastq.gz
## PRHU0018 14 unprocessed/PRHU0018_S16_R1_001.fastq.gz unprocessed/PRHU0018_S16_R2_001.fastq.gz
## hisat_count_table_hg38_115
## PRHU0001 preprocessing/PRHU0001/outputs/20250918hisat_hg38_115/hg38_115_genome-paired_s2_gene_ID_fcounts.csv.xz
## PRHU0002 preprocessing/PRHU0002/outputs/20250918hisat_hg38_115/hg38_115_genome-paired_s2_gene_ID_fcounts.csv.xz
## PRHU0009 preprocessing/PRHU0009/outputs/20250918hisat_hg38_115/hg38_115_genome-paired_s2_gene_ID_fcounts.csv.xz
## PRHU0010 preprocessing/PRHU0010/outputs/20250918hisat_hg38_115/hg38_115_genome-paired_s2_gene_ID_fcounts.csv.xz
## PRHU0011 preprocessing/PRHU0011/outputs/20250918hisat_hg38_115/hg38_115_genome-paired_s2_gene_ID_fcounts.csv.xz
## PRHU0018 preprocessing/PRHU0018/outputs/20250918hisat_hg38_115/hg38_115_genome-paired_s2_gene_ID_fcounts.csv.xz
## hisat_count_table_lpanamensis_mhomcol_v68
## PRHU0001 preprocessing/PRHU0001/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome-paired_s2_protein_coding_gene_ID_fcounts.csv.xz
## PRHU0002 preprocessing/PRHU0002/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome-paired_s2_protein_coding_gene_ID_fcounts.csv.xz
## PRHU0009 preprocessing/PRHU0009/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome-paired_s2_protein_coding_gene_ID_fcounts.csv.xz
## PRHU0010 preprocessing/PRHU0010/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome-paired_s2_protein_coding_gene_ID_fcounts.csv.xz
## PRHU0011 preprocessing/PRHU0011/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome-paired_s2_protein_coding_gene_ID_fcounts.csv.xz
## PRHU0018 preprocessing/PRHU0018/outputs/20250918hisat_lpanamensis_mhomcol_v68/lpanamensis_mhomcol_v68_genome-paired_s2_protein_coding_gene_ID_fcounts.csv.xz
## salmon_count_table_hg38_115
## PRHU0001 preprocessing/PRHU0001/outputs/80salmon_hg38_115_CDS/quant.sf
## PRHU0002 preprocessing/PRHU0002/outputs/80salmon_hg38_115_CDS/quant.sf
## PRHU0009 preprocessing/PRHU0009/outputs/80salmon_hg38_115_CDS/quant.sf
## PRHU0010 preprocessing/PRHU0010/outputs/80salmon_hg38_115_CDS/quant.sf
## PRHU0011 preprocessing/PRHU0011/outputs/80salmon_hg38_115_CDS/quant.sf
## PRHU0018 preprocessing/PRHU0018/outputs/80salmon_hg38_115_CDS/quant.sf
## salmon_count_table_lpanamensis_mhomcol_v68
## PRHU0001 preprocessing/PRHU0001/outputs/20250918salmon_lpanamensis_mhomcol_v68_CDS/quant.sf
## PRHU0002 preprocessing/PRHU0002/outputs/20250918salmon_lpanamensis_mhomcol_v68_CDS/quant.sf
## PRHU0009 preprocessing/PRHU0009/outputs/20250918salmon_lpanamensis_mhomcol_v68_CDS/quant.sf
## PRHU0010 preprocessing/PRHU0010/outputs/20250918salmon_lpanamensis_mhomcol_v68_CDS/quant.sf
## PRHU0011 preprocessing/PRHU0011/outputs/20250918salmon_lpanamensis_mhomcol_v68_CDS/quant.sf
## PRHU0018 preprocessing/PRHU0018/outputs/20250918salmon_lpanamensis_mhomcol_v68_CDS/quant.sf## [1] 40892 37639 47176 47162 46983 43731modified_meta[["detectionparasiteby7sl"]] <- sanitize_metadata(modified_meta[["detectionparasiteby7sl"]])
summary(modified_meta[["detectionparasiteby7sl"]])## negative notapplicable positive
## 63 29 11Create a factor of the 7SL detection of nasal samples. Note, we need to recast the NAs as undefined. I would have sworn that my gather function would do that?
modified_meta[["nasal_7sl_status"]] <- modified_meta[["detectionparasiteby7sl"]]
nasal_samples <- modified_meta[["sample_type"]] == "nasal swab"
summary(nasal_samples)## Mode FALSE TRUE
## logical 83 20## Mode FALSE TRUE
## logical 92 11## Mode FALSE TRUE
## logical 96 7nasal_positive_samples <- rownames(modified_meta)[nasal_positive]
nasal_positive_people <- modified_meta[nasal_positive_samples, "participant_code"]
nasal_positive_people## [1] "PP1009" "PP2020" "PP1009" "PP2005" "PP2006" "PP2019" "PP2020"nasal_positive_people_samples <- modified_meta[["participant_code"]] %in% nasal_positive_people
modified_meta[["nasal_7sl_status"]] <- "negative"
modified_meta[nasal_positive_people_samples, "nasal_7sl_status"] <- "positive"
write_xlsx(data = modified_meta, excel = "sample_sheets/human_samples_202511_with_nasal_factor.xlsx")## Deleting the file sample_sheets/human_samples_202511_with_nasal_factor.xlsx before writing the tables.## write_xlsx() wrote sample_sheets/human_samples_202511_with_nasal_factor.xlsx.
## The cursor is on sheet first, row: 106 column: 115.hisat_idx <- grep(pattern = "^hisat", x = names(first_spec))
second_spec <- first_spec[hisat_idx]
post_meta <- gather_preprocessing_metadata(
starting_metadata = pre_meta[["new_meta"]],
specification = second_spec, basedir = "preprocessing/202405", species = "hg38_111",
new_metadata = "sample_sheets/tmrc2_persistence_202405_lp_hg.xlsx")
both_meta <- gather_preprocessing_metadata(
starting_metadata = "sample_sheets/tmrc_persistence_202405.xlsx",
specification = first_spec,
basedir = "preprocessing/202405", species= c("lpanamensis_v68", "hg38_111"),
new_metadata = "sample_sheets/tmrc_persistence_202405_both.xlsx")6 Collect gene annotations
I should have all my load_xyz_annotation functions return some of the same elements in their retlists.
7 Quick peek at the SL samples, hg38 release 115
7.1 Gather the transcript and gene annotations.
7.2 Create initial hisat/salmon tables
hu_se_salmon <- create_se(modified_meta, gene_info = hg_tx,
tx_gene_map = hg_map, file_column = "salmon_count_table_hg38_115") %>%
set_conditions(fact = "sample_type") %>%
set_batches(fact = "library_type")## Reading the sample metadata.## Checking the state of the condition column.## Checking the state of the batch column.## Checking the condition factor.## The sample definitions comprises: 103 rows(samples) and 108 columns(metadata fields).## In some cases, (notably salmon) the format of the IDs used by this can be tricky.
## It is likely to require the transcript ID followed by a '.' and the ensembl column:
## 'transcript_version', which is explicitly different than the gene version column.
## If this is not correctly performed, very few genes will be observed## Rewriting the transcript<->gene map to remove tx versions.## reading in files with read_tsv## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103
## summarizing abundance
## summarizing counts
## summarizing length
## Matched 22263 annotations and counts.
## Some annotations were lost in merging, setting them to 'undefined'.
## Saving the summarized experiment to 'se.rda'.
## The final summarized experiment has 22263 rows and 108 columns.
## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## mRNA RZ
## 91 12hu_se_hisat_gene <- create_se(modified_meta, gene_info = hg_genes,
file_column = "hisat_count_table_hg38_115") %>%
set_conditions(fact = "sample_type") %>%
set_batches(fact = "library_type")## Reading the sample metadata.
## Checking the state of the condition column.
## Checking the state of the batch column.
## Checking the condition factor.
## The sample definitions comprises: 103 rows(samples) and 108 columns(metadata fields).
## Matched 21571 annotations and counts.
## Some annotations were lost in merging, setting them to 'undefined'.
## Saving the summarized experiment to 'se.rda'.
## The final summarized experiment has 21571 rows and 108 columns.
## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## mRNA RZ
## 91 127.3 Figure out which samples do not have 7SL categories
undef_7sl <- is.na(colData(hu_se_salmon)[["detectionparasiteby7sl"]])
colData(hu_se_salmon)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
colData(hu_se_hisat_gene)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
sample_7sl <- paste0(colData(hu_se_salmon)[["sample_type"]], "_",
colData(hu_se_salmon)[["detectionparasiteby7sl"]])
sample_7sl <- gsub(x = sample_7sl, pattern = "[[:space:]]", replacement = "_")
colData(hu_se_salmon)[["sample_7sl"]] <- sample_7sl
colData(hu_se_hisat_gene)[["sample_7sl"]] <- sample_7sl7.4 Healthy vs scar samples
7.5 Clean up missing 7SL detection samples
I think the last of these has been fixed since the last time I updated this sheet.
## Mode FALSE
## logical 103if (sum(undef_7sl)) {
colData(hu_se_salmon)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
colData(hu_se_hisat_gene)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
} else {
message("There appear to be no missing 7SL entries.")
}## There appear to be no missing 7SL entries.7.6 Print current state
##
## mRNA RZ
## 91 12##
## negative notapplicable positive
## 63 29 11##
## H-CL HD
## 100 37.7 Combine 7SL status and the sample type into one factor
7.8 Separate the mRNA samples from ribo-zero
Note, when we are finished, we will be using only the mRNA samples and ignoring the ribo-zero. But there are some questions about the data provided by the two libraries.
hu_se_salmon_mrna <- set_conditions(hu_se_salmon, fact = "sample_type") %>%
subset_se(subset = "library_type=='mRNA'") %>%
set_batches("detectionparasiteby7sl")## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## negative notapplicable positive
## 57 28 6hu_se_salmon_rz <- set_conditions(hu_se_salmon, fact = "sample_type") %>%
subset_se(subset = "library_type=='RZ'") %>%
set_batches("detectionparasiteby7sl")## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## negative notapplicable positive
## 6 1 5hu_se_hisat_gene_mrna <- set_conditions(hu_se_hisat_gene, fact = "sample_type") %>%
subset_se(subset = "library_type=='mRNA'") %>%
set_batches("detectionparasiteby7sl")## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## negative notapplicable positive
## 57 28 6hu_se_hisat_gene_rz <- set_conditions(hu_se_hisat_gene, fact = "sample_type") %>%
subset_se(subset = "library_type=='RZ'") %>%
set_batches("detectionparasiteby7sl")## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## negative notapplicable positive
## 6 1 57.9 Extract only the healthy of scar samples, only mRNA
hu_hs_salmon_mrna <- subset_se(hu_se_salmon, subset = "hs=='healthy'|hs=='scar'") %>%
set_conditions(fact = "hs")## The numbers of samples by condition are:##
## healthy scar
## 15 16hu_hs_hisat_mrna <- subset_se(hu_se_hisat_gene_mrna, subset = "hs=='healthy'|hs=='scar'") %>%
set_conditions(fact = "hs")## The numbers of samples by condition are:##
## healthy scar
## 15 158 HU Metadata
hu_mapped_mrna <- plot_metadata_factors(hu_se_hisat_gene_mrna, column = "hisat_genome_percent_log_hg38_115")
hu_mapped_mrna
hu_mapped_rz <- plot_metadata_factors(hu_se_hisat_gene_rz, column = "hisat_genome_percent_log_hg38_115")
hu_mapped_rz## Warning: Groups with fewer than two datapoints have been dropped.
## ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
hu_observed_mrna <- plot_metadata_factors(hu_se_hisat_gene_mrna, column = "salmon_observed_genes_hg38_115")
hu_observed_mrna
hu_observed_rz <- plot_metadata_factors(hu_se_hisat_gene_rz, column = "salmon_observed_genes_hg38_115")
hu_observed_rz## Warning: Groups with fewer than two datapoints have been dropped.
## ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
hu_pct_mrna <- plot_metadata_factors(hu_se_salmon_mrna, column = "salmon_percent_hg38_115")
hu_pct_mrna
## Warning: Groups with fewer than two datapoints have been dropped.
## ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
hu_sankey <- plot_meta_sankey(hu_se_salmon, factors = c("detectionparasiteby7sl", "sample_type", "library_type"))## Warning: attributes are not identical across measure variables; they will be dropped## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## ℹ The deprecated feature was likely used in the ggsankey package.
## Please report the issue at <https://github.com/davidsjoberg/ggsankey/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.## A sankey plot describing the metadata of 103 samples,
## including 30 out of 0 nodes and traversing metadata factors:
## detectionparasiteby7sl, sample_type, library_type.
9 nonzero/libsize/etc
## The colors used in the expressionset are: #1B9E77, #66A61E, #7570B3, #D95F02, #E6AB02, #E7298A.
## Library sizes of 103 samples,
## ranging from 2,281,699 to 14,374,842.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## ℹ The deprecated feature was likely used in the hpgltools package.
## Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.## A non-zero genes plot of 103 samples.
## These samples have an average 8.943 CPM coverage and 16231 genes observed, ranging from 15093 to
## 17527.## Warning: ggrepel: 56 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## Library sizes of 103 samples,
## ranging from 4,395,408 to 18,970,049.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## A non-zero genes plot of 103 samples.
## These samples have an average 12.61 CPM coverage and 15853 genes observed, ranging from 14800 to
## 17913.## Warning: ggrepel: 61 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## Library sizes of 91 samples,
## ranging from 6,563,145 to 18,970,049.
## Library sizes of 12 samples,
## ranging from 4,395,408 to 16,550,439.
10 Normalize
hu_sesn <- normalize(hu_se_salmon, transform = "log2", convert = "cpm",
filter = TRUE, norm = "quant")## Removing 4599 low-count genes (17664 remaining).## transform_counts: Found 200385 values equal to 0, adding 1 to the matrix.## A heatmap of pairwise sample correlations ranging from:
## 0.472624447742625 to 0.975818273903798.
hu_sesn_pca <- plot_pca(hu_sesn)
pp(file = "images/hu_pca_sampletype.png")
hu_sesn_pca$plot
dev.off()## png
## 2## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by nasal swab, PBMCs, skin biopsy healthy, skin biopsy non-lesion, skin biopsy scar, WBCs
## Shapes are defined by mRNA, RZ.
hu_detected <- subset_se(hu_se_salmon, subset = "detectionparasiteby7sl!='unknown'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
set_batches("sample_type")## The numbers of samples by condition are:##
## negative notapplicable positive
## 63 29 11## The number of samples by batch are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23hu_detect_nb <- normalize(hu_detected, transform = "log2", convert = "cpm",
filter = TRUE, batch = "svaseq")## Removing 4599 low-count genes (17664 remaining).## transform_counts: Found 64135 values less than 0.## transform_counts: Found 64135 values equal to 0, adding 1 to the matrix.## Warning in ggplot2::guide_legend(overwrite.aes = list(size = plot_size)): Arguments in `...` must be used.
## ✖ Problematic argument:
## • overwrite.aes = list(size = plot_size)
## ℹ Did you misspell an argument name?## png
## 2## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, notapplicable, positive
## Shapes are defined by nasal swab, PBMCs, skin biopsy healthy, skin biopsy non-lesion, skin biopsy scar, WBCs.
11 Compare distribution of RZ/Stranded libraries
Maria Adelaida is interested in the distribution of the relatively few rz samples vs the relatively large number of stranded mRNA libraries.
I think it is likely that the nasal samples are of primary interest.
salmon_mrna_7sl <- set_conditions(hu_se_salmon_mrna, fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 57 28 6salmon_mrna_7sl_norm <- normalize(salmon_mrna_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 5488 low-count genes (16775 remaining).## transform_counts: Found 64911 values equal to 0, adding 1 to the matrix.## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(salmon_mrna_7sl_norm)## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.## Warning in MASS::cov.trob(data[, vars], wt = weight * nrow(data)): Probable convergence failure
## Warning in MASS::cov.trob(data[, vars], wt = weight * nrow(data)): Probable convergence failure
salmon_mrna_7sl_nb <- normalize(salmon_mrna_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 5488 low-count genes (16775 remaining).## transform_counts: Found 20417 values less than 0.## transform_counts: Found 20417 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
hisat_mrna_7sl <- set_conditions(hu_se_hisat_gene_mrna, fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 57 28 6hisat_mrna_7sl_norm <- normalize(hisat_mrna_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 6173 low-count genes (15398 remaining).## transform_counts: Found 14191 values equal to 0, adding 1 to the matrix.## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(hisat_mrna_7sl_norm)## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.## Warning in MASS::cov.trob(data[, vars], wt = weight * nrow(data)): Probable convergence failure
## Warning in MASS::cov.trob(data[, vars], wt = weight * nrow(data)): Probable convergence failure
hisat_mrna_7sl_nb <- normalize(hisat_mrna_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 6173 low-count genes (15398 remaining).## transform_counts: Found 6654 values less than 0.## transform_counts: Found 6654 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
Now restrict to just the nasal samples.
salmon_nasal_mrna <- subset_se(hu_se_salmon_mrna, subset = "sample_type=='nasal swab'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 8 1 2salmon_nasal_mrna_norm <- normalize(salmon_nasal_mrna, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 8374 low-count genes (13889 remaining).## transform_counts: Found 2353 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
salmon_nasal_mrna_nb <- normalize(salmon_nasal_mrna, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 8374 low-count genes (13889 remaining).## transform_counts: Found 841 values less than 0.## transform_counts: Found 841 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
hisat_nasal_mrna <- subset_se(hu_se_hisat_gene_mrna, subset = "sample_type=='nasal swab'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 8 1 2hisat_nasal_mrna_norm <- normalize(hisat_nasal_mrna, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 8412 low-count genes (13159 remaining).## transform_counts: Found 12 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
hisat_nasal_mrna_nb <- normalize(hisat_nasal_mrna, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 8412 low-count genes (13159 remaining).## transform_counts: Found 108 values less than 0.## transform_counts: Found 108 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
11.1 Repeat with the ribo zero samples
salmon_rz_7sl <- set_conditions(hu_se_salmon_rz, fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 6 1 5salmon_rz_7sl_norm <- normalize(salmon_rz_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 6360 low-count genes (15903 remaining).## transform_counts: Found 8271 values equal to 0, adding 1 to the matrix.## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(salmon_rz_7sl_norm)## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
salmon_rz_7sl_nb <- normalize(salmon_rz_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 6360 low-count genes (15903 remaining).## transform_counts: Found 1964 values less than 0.## transform_counts: Found 1964 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
hisat_rz_7sl <- set_conditions(hu_se_hisat_gene_rz, fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 6 1 5hisat_rz_7sl_norm <- normalize(hisat_rz_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 7116 low-count genes (14455 remaining).## transform_counts: Found 306 values equal to 0, adding 1 to the matrix.## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(hisat_rz_7sl_norm)## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
hisat_rz_7sl_nb <- normalize(hisat_rz_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 7116 low-count genes (14455 remaining).## transform_counts: Found 322 values less than 0.## transform_counts: Found 322 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
Now restrict to just the nasal samples.
salmon_nasal_rz <- subset_se(hu_se_salmon_rz, subset = "sample_type=='nasal swab'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 3 1 5salmon_nasal_rz_norm <- normalize(salmon_nasal_rz, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 7557 low-count genes (14706 remaining).## transform_counts: Found 2498 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
salmon_nasal_rz_nb <- normalize(salmon_nasal_rz, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 7557 low-count genes (14706 remaining).## transform_counts: Found 1303 values less than 0.## transform_counts: Found 1303 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
hisat_nasal_rz <- subset_se(hu_se_hisat_gene_rz, subset = "sample_type=='nasal swab'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## The numbers of samples by condition are:##
## negative notapplicable positive
## 3 1 5hisat_nasal_rz_norm <- normalize(hisat_nasal_rz, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Removing 8212 low-count genes (13359 remaining).## transform_counts: Found 9 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
hisat_nasal_rz_nb <- normalize(hisat_nasal_rz, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Removing 8212 low-count genes (13359 remaining).## transform_counts: Found 137 values less than 0.## transform_counts: Found 137 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by negative, positive.
12 Look at sample type and 7sl
## The numbers of samples by condition are:##
## nasal swab_negative nasal swab_notapplicable nasal swab_positive PBMCs_notapplicable
## 8 1 2 25
## skin biopsy healthy_negative skin biopsy healthy_notapplicable skin biopsy non-lesion_negative skin biopsy scar_negative
## 14 1 2 14
## skin biopsy scar_notapplicable WBCs_negative WBCs_positive
## 1 19 4hu_nasal <- subset_se(hu_s7sl, subset = "sample_type=='nasal swab'")
hu_nasal_nb <- normalize(hu_nasal, transform = "log2", convert = "cpm",
batch = "svaseq", filter = TRUE)## Removing 8223 low-count genes (14040 remaining).## transform_counts: Found 1045 values less than 0.## transform_counts: Found 1045 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by nasal swab_negative, nasal swab_notapplicable, nasal swab_positive
## Shapes are defined by negative, notapplicable, positive.## png
## 2hu_wbc <- subset_se(hu_s7sl, subset = "sample_type=='WBCs'")
hu_wbc_nb <- normalize(hu_wbc, transform = "log2", convert = "cpm",
batch = "svaseq", filter = TRUE)## Removing 8982 low-count genes (13281 remaining).## transform_counts: Found 2601 values less than 0.## transform_counts: Found 2601 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by WBCs_negative, WBCs_positive
## Shapes are defined by negative, positive.## png
## 2short_factor <- gsub(x = as.character(colData(hu_nasal)[["condition"]]), pattern = ".*_(.*)$", replacement = "\\1")
hu_nasal <- set_conditions(hu_nasal, fact = as.factor(short_factor))## The numbers of samples by condition are:##
## negative notapplicable positive
## 8 1 2hu_nasal_np <- subset_se(hu_nasal, subset = "condition!='notapplicable'")
hu_nasal_de <- all_pairwise(hu_nasal_np, filter = TRUE, force = TRUE,
model_fstring = "~ 0 + condition", model_svs = "svaseq")## negative positive
## 8 2## Removing 8374 low-count genes (13889 remaining).## Basic step 0/3: Normalizing data.## Basic step 0/3: Converting data.## I think this is failing? SummarizedExperiment## Basic step 0/3: Transforming data.## Setting 6305 entries to zero.## Warning in choose_binom_dataset(input, force = force): This data was inappropriately forced into integers.## This received a matrix of SVs.## converting counts to integer mode## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## Warning in choose_binom_dataset(input, force = force): This data was inappropriately forced into integers.
## Warning in choose_binom_dataset(input, force = force): This data was inappropriately forced into integers.
## Warning in choose_binom_dataset(input, force = force): This data was inappropriately forced into integers.## conditions
## negative positive
## 8 2## conditions
## negative positive
## 8 2## Warning in choose_binom_dataset(input, force = force): This data was inappropriately forced into integers.## conditions
## negative positive
## 8 2## A pairwise differential expression with results from: basic, deseq, ebseq, edger, limma, noiseq.## This used a surrogate/batch estimate from: svaseq.## The primary analysis performed 1 comparisons.## The logFC agreement among the methods follows:## pstv_vs_ng
## basic_vs_deseq 0.52525
## basic_vs_dream 0.70791
## basic_vs_ebseq 0.67788
## basic_vs_edger 0.60628
## basic_vs_limma 0.71872
## basic_vs_noiseq 0.11718
## deseq_vs_dream 0.69773
## deseq_vs_ebseq 0.74945
## deseq_vs_edger 0.90410
## deseq_vs_limma 0.65985
## deseq_vs_noiseq 0.33641
## dream_vs_ebseq 0.69816
## dream_vs_edger 0.80879
## dream_vs_limma 0.97772
## dream_vs_noiseq 0.09634
## ebseq_vs_edger 0.80917
## ebseq_vs_limma 0.68784
## ebseq_vs_noiseq 0.54862
## edger_vs_limma 0.76926
## edger_vs_noiseq 0.33872
## limma_vs_noiseq 0.10929## Deleting the file excel/persist_table.xlsx before writing the tables.## Looking for subscript invalid names, start of extract_keepers.## Looking for subscript invalid names, end of extract_keepers.## A set of combined differential expression results.## table deseq_sigup deseq_sigdown edger_sigup edger_sigdown limma_sigup limma_sigdown
## 1 positive_vs_negative 21 69 19 69 0 0## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## ℹ The deprecated feature was likely used in the UpSetR package.
## Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.## `geom_line()`: Each group consists of only one observation.
## ℹ Do you need to adjust the group aesthetic?## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## ℹ The deprecated feature was likely used in the UpSetR package.
## Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.## Plot describing unique/shared genes in a differential expression table.
## Deleting the file excel/persist_sig.xlsx before writing the tables.## A set of genes deemed significant according to limma, edger, deseq, ebseq, basic.## The parameters defining significant were:## LFC cutoff: 1 adj P cutoff: 0.05## limma_up limma_down edger_up edger_down deseq_up deseq_down ebseq_up ebseq_down basic_up basic_down
## positive_vs_negative 0 0 19 69 21 69 85 54 0 0
13 Healthy vs Scar samples
One query from our last meeting which I forgot about until I reread my TODO notes: compare the samples marked as healthy compared to those marked as scar. These are two distantly separate skin biopsies of the same person.
hu_hs_de <- all_pairwise(hu_hs, filter = TRUE, force = TRUE,
model_svs = "svaseq", model_fstring = "~ 0 + condition")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'hu_hs' not found## Deleting the file excel/healthy_vs_scar_table.xlsx before writing the tables.## Error: object 'hu_hs_de' not found## Error: object 'hu_hs_table' not found## Deleting the file excel/healthy_vs_scar_sig.xlsx before writing the tables.## Error: object 'hu_hs_table' not found## Error: object 'hu_hs_sig' not found14 Take a peek at the kraken results
hu_kraken_viral <- create_se(pre_meta[["new_meta"]], file_column = "kraken_matrix_viral",
handle_na = "zero")## Reading the sample metadata.## Checking the state of the condition column.## Checking the state of the batch column.## Checking the condition factor.## The sample definitions comprises: 103 rows(samples) and 107 columns(metadata fields).## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0002/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0009/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0010/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0011/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0018/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0019/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0020/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0012/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0013/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0014/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0021/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0022/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0023/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0015/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0016/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0017/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0024/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0025/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0026/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0038/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0006/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0007/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0008/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0005/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0004/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0003/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0027/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0028/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0029/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0030/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0031/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0032/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0035/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0033/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0034/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0036/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0037/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0039/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0040/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0041/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0042/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0043/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0044/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0045/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0046/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0047/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0048/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0049/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0050/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0051/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0052/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0053/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0054/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0055/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0056/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0057/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0058/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0059/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0060/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0061/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0062/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0063/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0064/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0065/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0066/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0067/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0068/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0069/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0070/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0071/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0072/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0073/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0074/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0075/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0076/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0077/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0078/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0079/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0080/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0081/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0082/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0083/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0084/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0085/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0086/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0087/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0088/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0089/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0090/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0091/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0092/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0093/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0094/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0095/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0096/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0097/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0098/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0099/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0100/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0101/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0102/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0103/outputs/20250918kraken_viral/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in create_se(pre_meta[["new_meta"]], file_column = "kraken_matrix_viral", : There are some NAs in this data, the 'handle_nas'
## parameter may be required.## Matched 487 annotations and counts.## Saving the summarized experiment to 'se.rda'.## The final summarized experiment has 487 rows and 107 columns.hu_kraken_viral <- set_conditions(hu_kraken_viral, fact = "sample_type") %>%
set_batches("detectionparasiteby7sl")## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## negative positive unknown
## 63 11 29## Removing 0 low-count genes (487 remaining).## Did not recognize the normalization, leaving the table alone.
## Recognized normalizations include: 'qsmooth', 'sf', 'sf2', 'vsd', 'quant',
## 'tmm', 'qsmooth_median', 'upperquartile', and 'rle.'## transform_counts: Found 45295 values equal to 0, adding 1 to the matrix.## A heatmap of pairwise sample correlations ranging from:
## 0.745956883236431 to 0.973829842329974.
## A heatmap of pairwise sample distances ranging from:
## 7.3460130601336 to 25.9738855355352.
## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by nasal swab, PBMCs, skin biopsy healthy, skin biopsy non-lesion, skin biopsy scar, WBCs
## Shapes are defined by negative, positive, unknown.
nasal_kraken <- subset_se(hu_kraken_viral, subset = "condition=='nasal swab'")
nasal_norm <- normalize(nasal_kraken_viral, filter = TRUE, norm = "cpm", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'nasal_kraken_viral' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'input_data' in selecting a method for function 'plot_heatmap': object 'nasal_norm' not foundhu_kraken_bacteria <- create_se(pre_meta[["new_meta"]], file_column = "kraken_matrix_bacterial",
handle_na = "zero")## Reading the sample metadata.## Checking the state of the condition column.## Checking the state of the batch column.## Checking the condition factor.## The sample definitions comprises: 103 rows(samples) and 107 columns(metadata fields).## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0002/outputs/02kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0009/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0010/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0011/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0018/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0019/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0020/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0012/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0013/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0014/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0021/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0022/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0023/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0015/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0016/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0017/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0024/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0025/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0026/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0038/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0006/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0007/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0008/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0005/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0004/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0003/outputs/02kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0027/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0028/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0029/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0030/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0031/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0032/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0035/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0033/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0034/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0036/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0037/outputs/06kraken_bacteria/kraken_report_matrix.tsv has mismatched
## rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0039/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0040/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0041/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0042/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0043/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0044/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0045/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0046/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0047/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0048/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0049/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0050/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0051/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0052/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0053/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0054/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0055/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0056/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0057/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0058/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0059/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0060/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0061/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0062/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0063/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0064/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0065/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0066/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0067/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0068/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0069/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0070/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0071/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0072/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0073/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0074/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0075/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0076/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0077/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0078/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0079/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0080/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0081/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0082/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0083/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0084/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0085/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0086/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0087/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0088/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0089/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0090/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0091/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0092/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0093/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0094/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0095/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0096/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0097/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0098/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0099/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0100/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0101/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0102/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in first_rownames != current_rownames: longer object length is not a multiple of shorter object length## Warning in read_counts(ids, files, countdir = countdir, file_type = file_type, : The file:
## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0103/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
## mismatched rownames.## Warning in create_se(pre_meta[["new_meta"]], file_column = "kraken_matrix_bacterial", : There are some NAs in this data, the 'handle_nas'
## parameter may be required.## Matched 1754 annotations and counts.## Saving the summarized experiment to 'se.rda'.## The final summarized experiment has 1754 rows and 107 columns.hu_kraken_bacteria <- set_conditions(hu_kraken_bacteria, fact = "sample_type") %>%
set_batches("detectionparasiteby7sl")## The numbers of samples by condition are:##
## nasal swab PBMCs skin biopsy healthy skin biopsy non-lesion skin biopsy scar WBCs
## 20 25 15 4 16 23## The number of samples by batch are:##
## negative positive unknown
## 63 11 29## Error: object 'kraken_bacteria' not foundkraken_bacteria_norm <- normalize(hu_kraken_bacteria, filter = TRUE, norm = "cpm", transform = "log2")## Removing 0 low-count genes (1754 remaining).## Did not recognize the normalization, leaving the table alone.
## Recognized normalizations include: 'qsmooth', 'sf', 'sf2', 'vsd', 'quant',
## 'tmm', 'qsmooth_median', 'upperquartile', and 'rle.'## transform_counts: Found 88803 values equal to 0, adding 1 to the matrix.## A heatmap of pairwise sample correlations ranging from:
## 0.604850876191328 to 0.934803391036582.
## A heatmap of pairwise sample distances ranging from:
## 38.2027362700424 to 129.211351296268.
## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by nasal swab, PBMCs, skin biopsy healthy, skin biopsy non-lesion, skin biopsy scar, WBCs
## Shapes are defined by negative, positive, unknown.## Warning in MASS::cov.trob(data[, vars], wt = weight * nrow(data)): Probable convergence failure## Warning in MASS::cov.trob(data[, vars], wt = weight * nrow(data)): Probable convergence failure
15 Nasal as a proxy for everything else
In the beginning of this document, I created a peculiar factor out of the nasal sample 7SL state and applied its result to every other sample for each person; thus a person who was positive for the nasal sample was deemed positive for everything. Let us see what that looks like…
## The numbers of samples by condition are:##
## negative positive
## 84 19## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_genes' not foundnasal_7sl_se_nb <- normalize(nasal_7sl_se, transform = "log2", convert = "cpm", filter = TRUE,
batch = "svaseq")## Removing 4599 low-count genes (17664 remaining).## transform_counts: Found 43532 values less than 0.## transform_counts: Found 43532 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by mRNA, RZ.
nasal_7sl_de <- all_pairwise(nasal_7sl_se, filter = TRUE,
model_svs = "svaseq", model_fstring = "~ 0 + condition")## negative positive
## 84 19## Removing 4599 low-count genes (17664 remaining).## Basic step 0/3: Normalizing data.## Basic step 0/3: Converting data.## I think this is failing? SummarizedExperiment## Basic step 0/3: Transforming data.## Setting 440621 entries to zero.## This received a matrix of SVs.## Error in DESeqDataSet(se, design = design, ignoreRank) :
## some values in assay are not integers## conditions
## negative positive
## 84 19## conditions
## negative positive
## 84 19## conditions
## negative positive
## 84 19## A pairwise differential expression with results from: basic, deseq, ebseq, edger, limma, noiseq.## This used a surrogate/batch estimate from: svaseq.## The primary analysis performed 1 comparisons.## The logFC agreement among the methods follows:## pstv_vs_ng
## basic_vs_dream 0.5423
## basic_vs_ebseq 0.5845
## basic_vs_edger 0.4407
## basic_vs_limma 0.6008
## basic_vs_noiseq 0.5254
## dream_vs_ebseq 0.5379
## dream_vs_edger 0.6983
## dream_vs_limma 0.9815
## dream_vs_noiseq 0.6734
## ebseq_vs_edger 0.7371
## ebseq_vs_limma 0.5669
## ebseq_vs_noiseq 0.7698
## edger_vs_limma 0.6834
## edger_vs_noiseq 0.7224
## limma_vs_noiseq 0.6947nasal_7sl_hisat_de <- all_pairwise(nasal_7sl_hisat_se, filter = TRUE,
model_svs = "svaseq", model_fstring = "~ 0 + condition")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'nasal_7sl_hisat_se' not found## Error: object 'nasal_7sl_hisat_de' not found## Looking for subscript invalid names, start of extract_keepers.## Looking for subscript invalid names, end of extract_keepers.## A set of combined differential expression results.## table deseq_sigup deseq_sigdown edger_sigup edger_sigdown limma_sigup limma_sigdown
## 1 positive_vs_negative 0 0 26 49 80 54## Only has information, cannot create an UpSet.## Plot describing unique/shared genes in a differential expression table.## NULLnasal_7sl_hisat_table <- combine_de_tables(nasal_7sl_hisat_de, excel = "excel/nasal_7sl_proxy_table.xlsx")## Deleting the file excel/nasal_7sl_proxy_table.xlsx before writing the tables.## Error: object 'nasal_7sl_hisat_de' not found## Error: object 'nasal_7sl_hisat_table' not foundOh, Maria Adelaida was actually looking only for the PBMC samples.
pbmc_nasal_7sl_se <- subset_se(hu_se_salmon, subset = "condition=='PBMCs'") %>%
set_conditions(fact = "nasal_7sl_status")## The numbers of samples by condition are:##
## negative positive
## 21 4pbmc_nasal_7sl_hisat_se <- subset_se(hu_se_hisat_gene, subset = "condition=='PBMCs'") %>%
set_conditions(fact = "nasal_7sl_status")## The numbers of samples by condition are:##
## negative positive
## 21 4pbmc_nasal_hisat_norm <- normalize(pbmc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
norm = "quant", filter = TRUE)## Removing 9124 low-count genes (12447 remaining).## transform_counts: Found 39 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by mRNA.
pbmc_nasal_hisat_nb <- normalize(pbmc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
batch = "svaseq", filter = "simple")## Removing 3931 low-count genes (17640 remaining).## transform_counts: Found 20961 values less than 0.## transform_counts: Found 20961 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by mRNA.
pbmc_nasal_7sl_de <- all_pairwise(pbmc_nasal_7sl_se, filter = "simple",
model_svs = "svaseq", model_fstring = "~ 0 + condition")## negative positive
## 21 4## Removing 3479 low-count genes (18784 remaining).## Basic step 0/3: Normalizing data.## Basic step 0/3: Converting data.## I think this is failing? SummarizedExperiment## Basic step 0/3: Transforming data.## Setting 140680 entries to zero.## This received a matrix of SVs.## Error in DESeqDataSet(se, design = design, ignoreRank) :
## some values in assay are not integers## conditions
## negative positive
## 21 4## conditions
## negative positive
## 21 4## conditions
## negative positive
## 21 4## Looking for subscript invalid names, start of extract_keepers.## Looking for subscript invalid names, end of extract_keepers.16 TODO 202512
Repeat this nasal proxy test using each of the other cell types.
The factors of likely interest are: “wbcs” “nasal swab” ideally both “skin biopsy healthy” and “skin biopsy scar” but perhaps only “skin biopsy”.
wbc_nasal_7sl_se <- subset_se(hu_se_salmon, subset = "condition=='WBCs'") %>%
set_conditions(fact = "nasal_7sl_status")## The numbers of samples by condition are:##
## negative positive
## 19 4wbc_nasal_7sl_hisat_se <- subset_se(hu_se_hisat_gene, subset = "condition=='WBCs'") %>%
set_conditions(fact = "nasal_7sl_status")## The numbers of samples by condition are:##
## negative positive
## 19 4wbc_nasal_hisat_norm <- normalize(wbc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
filter = "simple", norm = "quant")## Removing 4161 low-count genes (17410 remaining).## transform_counts: Found 52115 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by mRNA.
wbc_nasal_hisat_nb <- normalize(wbc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
filter = "simple", batch = "svaseq")## Removing 4161 low-count genes (17410 remaining).## transform_counts: Found 19565 values less than 0.## transform_counts: Found 19565 values equal to 0, adding 1 to the matrix.## The result of performing a fast_svd dimension reduction.
## The x-axis is PC1 and the y-axis is PC2
## Colors are defined by negative, positive
## Shapes are defined by mRNA.
wbc_nasal_7sl_de <- all_pairwise(wbc_nasal_7sl_se, filter = "simple",
model_svs = "svaseq", model_fstring = "~ 0 + condition")## negative positive
## 19 4## Removing 3727 low-count genes (18536 remaining).## Basic step 0/3: Normalizing data.## Basic step 0/3: Converting data.## I think this is failing? SummarizedExperiment## Basic step 0/3: Transforming data.## Setting 130319 entries to zero.## This received a matrix of SVs.## Error in DESeqDataSet(se, design = design, ignoreRank) :
## some values in assay are not integers## conditions
## negative positive
## 19 4## conditions
## negative positive
## 19 4## conditions
## negative positive
## 19 4## Looking for subscript invalid names, start of extract_keepers.## Looking for subscript invalid names, end of extract_keepers.---
title: "Examining human samples"
author: "atb abelew@gmail.com"
date: "`r Sys.Date()`"
bibliography: atb.bib
output:
  html_document:
    code_download: true
    code_folding: show
    fig_caption: true
    fig_height: 7
    fig_width: 7
    highlight: zenburn
    keep_md: false
    mode: selfcontained
    number_sections: true
    self_contained: true
    theme: readable
    toc: true
    toc_float:
      collapsed: false
      smooth_scroll: false
---

<style type="text/css">
body, td {
  font-size: 16px;
}
code.r{
  font-size: 16px;
}
pre {
  font-size: 16px
}
body .main-container {
  max-width: 1600px;
}
</style>

```{r options, include=FALSE}
library(hpgltools)
library(ggplot2)
library(reticulate)
tt <- try(devtools::load_all("~/hpgltools"))
knitr::opts_knit$set(
  progress = TRUE, verbose = TRUE, width = 90, echo = TRUE)
knitr::opts_chunk$set(
  error = TRUE, fig.width = 8, fig.height = 8, fig.retina = 2,
  out.width = "100%", dev = "png",
  dev.args = list(png = list(type = "cairo-png")))
old_options <- options(digits = 4, stringsAsFactors = FALSE, knitr.duplicate.label = "allow")
ggplot2::theme_set(ggplot2::theme_bw(base_size = 12))
ver <- "202405"
previous_file <- ""
ver <- format(Sys.Date(), "%Y%m%d")

##tmp <- sm(loadme(filename=paste0(gsub(pattern="\\.Rmd", replace="", x=previous_file), "-v", ver, ".rda.xz")))
rmd_file <- "human_samples_2025.Rmd"
```

# TODO

## 202511

1.  We have some samples which are defined as persistent via 7SL.  Can
    we see some reads in those samples?
2.  Send file with mapped reads per sample for all human samples.
3.  Queue SL read counter for all human samples.
4.  All samples have nasal, skin, PBMC; all patients are nasal + or
    nasal -; perform contrasts of nasal+/nasal- of the PBMC samples.
    For the PBMC samples, recast them as +/-

## 202601

1.  7SL positive vs negative for
2.  Add plot of transcriptome clustering of nasal swabs between nasal
    positive/negative with the caveat that the are only 2 positives, 8
    negatives, and 1 undetermined in the stranded library; the
    ribozero have 5 positive, 3 negative, and 1 undetermined.
3.  Create a relative abundance of bacteria/viruses observed in the
    nassal samples; counting at genus.

Note that this requires splitting the data into 4 groups: salmon+rz,
salmon+mrna, hisat+rz, hisat+mrna.

# Changelog

## 202511

Following my conversation with Maria Adelaida, I downloaded a new copy
of our online sample sheet and made a sub-copy with only the human
samples.  It is named (creatively) sample_sheets/human_samples_202511.xlsx

# Introduction

I want to use this document to examine our first round of persistence
samples.  I checked my email from Najib and did not find a sample
sheet but did find an explanation of the three sample types we expect.

In preparation for this, I downloaded a new hg38 genome.  Since the
panamensis asembly has not significantly changed (excepting the
putative long read genome which I have not yet seen), I am just using
the same one.

# Loading annotation

The hg38 genome I got is brand new (202405), so do not use the archive
for a while.

```{r}
## Ok, so useast.ensembl is failing today, let us use the jan2024 archive?
#hs_annot <- load_biomart_annotations(archive = FALSE, species = "hsapiens")
## Seems like the 202401 archive is a good choice, it is explicitly the hg38_111 release.
## and it is waaaaay faster (like 100x) than useast right now.
hs_annot <- load_biomart_annotations(archive = FALSE, species = "hsapiens", overwrite = TRUE,
                                     year = 2025, month = "08")

panamensis_orgdb_idx <- grep(pattern = "^org.+panamen.+MHOM.+db$", x = rownames(installed.packages()))
panamensis_orgdb <- tail(rownames(installed.packages())[panamensis_orgdb_idx], n = 1)
lp_annot <- load_orgdb_annotations(panamensis_orgdb, keytype = "gid")
```

This is a little silly, but I am going to reload the annotations using
the previous invocation to extract the annotation table without having
to think.  The previous block loads the orgdb for me, so I can just
use that to get the fun annotations.

```{r}
lp_annot <- load_orgdb_annotations(panamensis_orgdb, keytype = "gid", fields = "^annot")
```

# Collect preprocessed metadata

Use my new sample sheet here.

```{r}
current_samplesheet <- "sample_sheets/human_samples_202511.xlsx"
first_spec <- make_rnaseq_spec()
input <- read_metadata(current_samplesheet)
colnames(input)

pre_meta <- gather_preprocessing_metadata(
  starting_metadata = current_samplesheet, id_column = "hpgl_identifier",
  specification = first_spec, new_metadata = "persistence_hu_modified.xlsx",
  basedir = "preprocessing", species = c("hg38_115", "lpanamensis_mhomcol_v68"))

modified_meta <- pre_meta[["new_meta"]]
## Added the following line to gather_preprocessing_metadata()
rownames(modified_meta) <- make.names(modified_meta[["hpgl_identifier"]], unique = TRUE)

## FIXME: 202511: I broke something in some of these functions and it is pulling
## the wrong information for number of observed genes.
head(modified_meta)
head(modified_meta[["salmon_observed_genes_hg38_115"]])

modified_meta[["detectionparasiteby7sl"]] <- sanitize_metadata(modified_meta[["detectionparasiteby7sl"]])
summary(modified_meta[["detectionparasiteby7sl"]])

```

Create a factor of the 7SL detection of nasal samples.  Note, we need
to recast the NAs as undefined.  I would have sworn that my gather
function would do that?

```{r}
modified_meta[["nasal_7sl_status"]] <- modified_meta[["detectionparasiteby7sl"]]

nasal_samples <- modified_meta[["sample_type"]] == "nasal swab"
summary(nasal_samples)
sl_positive <- modified_meta[["nasal_7sl_status"]] == "positive"
summary(sl_positive)
nasal_positive <- nasal_samples & sl_positive
summary(nasal_positive)
nasal_positive_samples <- rownames(modified_meta)[nasal_positive]
nasal_positive_people <- modified_meta[nasal_positive_samples, "participant_code"]
nasal_positive_people
nasal_positive_people_samples <- modified_meta[["participant_code"]] %in% nasal_positive_people
modified_meta[["nasal_7sl_status"]] <- "negative"
modified_meta[nasal_positive_people_samples, "nasal_7sl_status"] <- "positive"
write_xlsx(data = modified_meta, excel = "sample_sheets/human_samples_202511_with_nasal_factor.xlsx")
```

```{r, eval=FALSE}
hisat_idx <- grep(pattern = "^hisat", x = names(first_spec))
second_spec <- first_spec[hisat_idx]
post_meta <- gather_preprocessing_metadata(
  starting_metadata = pre_meta[["new_meta"]],
  specification = second_spec, basedir = "preprocessing/202405", species = "hg38_111",
  new_metadata = "sample_sheets/tmrc2_persistence_202405_lp_hg.xlsx")

both_meta <- gather_preprocessing_metadata(
  starting_metadata = "sample_sheets/tmrc_persistence_202405.xlsx",
  specification = first_spec,
  basedir = "preprocessing/202405", species= c("lpanamensis_v68", "hg38_111"),
  new_metadata = "sample_sheets/tmrc_persistence_202405_both.xlsx")
```

# Collect gene annotations

I should have all my load_xyz_annotation functions return some of the
same elements in their retlists.

```{r}
lp_genes <- lp_annot[["genes"]]
hg_genes <- hs_annot[["gene_annotations"]]
```

# Quick peek at the SL samples, hg38 release 115

## Gather the transcript and gene annotations.

```{r}
hg_tx <- hs_annot[["annotation"]]
hg_map <- hs_annot[["gene_tx_map"]]
lp_genes <- lp_annot[["genes"]]
```

## Create initial hisat/salmon tables

```{r}
hu_se_salmon <- create_se(modified_meta, gene_info = hg_tx,
                          tx_gene_map = hg_map, file_column = "salmon_count_table_hg38_115") %>%
  set_conditions(fact = "sample_type") %>%
  set_batches(fact = "library_type")
hu_se_hisat_gene <- create_se(modified_meta, gene_info = hg_genes,
                              file_column = "hisat_count_table_hg38_115") %>%
  set_conditions(fact = "sample_type") %>%
  set_batches(fact = "library_type")
```

## Figure out which samples do not have 7SL categories

```{r}
undef_7sl <- is.na(colData(hu_se_salmon)[["detectionparasiteby7sl"]])
colData(hu_se_salmon)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
colData(hu_se_hisat_gene)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
sample_7sl <- paste0(colData(hu_se_salmon)[["sample_type"]], "_",
                     colData(hu_se_salmon)[["detectionparasiteby7sl"]])
sample_7sl <- gsub(x = sample_7sl, pattern = "[[:space:]]", replacement = "_")
colData(hu_se_salmon)[["sample_7sl"]] <- sample_7sl
colData(hu_se_hisat_gene)[["sample_7sl"]] <- sample_7sl
```

## Healthy vs scar samples

```{r}
healthy_vs_scar <- gsub(x = colData(hu_se_salmon)[["sample_type"]],
                        pattern = "^skin biopsy ", replacement = "")
colData(hu_se_salmon)[["hs"]] <- healthy_vs_scar
colData(hu_se_hisat_gene)[["hs"]] <- healthy_vs_scar
```

## Clean up missing 7SL detection samples

I think the last of these has been fixed since the last time I updated
this sheet.

```{r}
undef_7sl <- is.na(colData(hu_se_hisat_gene)[["detectionparasiteby7sl"]])
summary(undef_7sl)
if (sum(undef_7sl)) {
  colData(hu_se_salmon)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
  colData(hu_se_hisat_gene)[undef_7sl, "detectionparasiteby7sl"] <- "unknown"
} else {
  message("There appear to be no missing 7SL entries.")
}
```

## Print current state

```{r}
table(colData(hu_se_hisat_gene)[["library_type"]])
table(colData(hu_se_hisat_gene)[["detectionparasiteby7sl"]])
table(colData(hu_se_hisat_gene)[["clinical_presentation"]])
```

## Combine 7SL status and the sample type into one factor

```{r}
sample_7sl <- paste0(colData(hu_se_hisat_gene)[["sample_type"]], "_",
                     colData(hu_se_hisat_gene)[["detectionparasiteby7sl"]])
colData(hu_se_hisat_gene)[["sample_7sl"]] <- sample_7sl
colData(hu_se_salmon)[["sample_7sl"]] <- sample_7sl
```

## Separate the mRNA samples from ribo-zero

Note, when we are finished, we will be using only the mRNA samples and
ignoring the ribo-zero.  But there are some questions about the data
provided by the two libraries.

```{r}
hu_se_salmon_mrna <- set_conditions(hu_se_salmon, fact = "sample_type") %>%
  subset_se(subset = "library_type=='mRNA'") %>%
  set_batches("detectionparasiteby7sl")
hu_se_salmon_rz <- set_conditions(hu_se_salmon, fact = "sample_type") %>%
  subset_se(subset = "library_type=='RZ'") %>%
  set_batches("detectionparasiteby7sl")

hu_se_hisat_gene_mrna <- set_conditions(hu_se_hisat_gene, fact = "sample_type") %>%
  subset_se(subset = "library_type=='mRNA'") %>%
  set_batches("detectionparasiteby7sl")
hu_se_hisat_gene_rz <- set_conditions(hu_se_hisat_gene, fact = "sample_type") %>%
  subset_se(subset = "library_type=='RZ'") %>%
  set_batches("detectionparasiteby7sl")
```

## Extract only the healthy of scar samples, only mRNA

```{r}
hu_hs_salmon_mrna <- subset_se(hu_se_salmon, subset = "hs=='healthy'|hs=='scar'") %>%
  set_conditions(fact = "hs")
hu_hs_hisat_mrna <- subset_se(hu_se_hisat_gene_mrna, subset = "hs=='healthy'|hs=='scar'") %>%
  set_conditions(fact = "hs")
```

# HU Metadata

```{r}
hu_mapped_mrna <- plot_metadata_factors(hu_se_hisat_gene_mrna, column = "hisat_genome_percent_log_hg38_115")
hu_mapped_mrna

hu_mapped_rz <- plot_metadata_factors(hu_se_hisat_gene_rz, column = "hisat_genome_percent_log_hg38_115")
hu_mapped_rz

hu_observed_mrna <- plot_metadata_factors(hu_se_hisat_gene_mrna, column = "salmon_observed_genes_hg38_115")
hu_observed_mrna

hu_observed_rz <- plot_metadata_factors(hu_se_hisat_gene_rz, column = "salmon_observed_genes_hg38_115")
hu_observed_rz

hu_pct_mrna <- plot_metadata_factors(hu_se_salmon_mrna, column = "salmon_percent_hg38_115")
hu_pct_mrna

hu_pct_rz <- plot_metadata_factors(hu_se_salmon_rz, column = "salmon_percent_hg38_115")
hu_pct_rz

hu_sankey <- plot_meta_sankey(hu_se_salmon, factors = c("detectionparasiteby7sl", "sample_type", "library_type"))
hu_sankey
```

# nonzero/libsize/etc

```{r}
plot_legend(hu_se_salmon)
plot_libsize(hu_se_salmon)
plot_nonzero(hu_se_salmon, y_intercept = 0.75)

plot_libsize(hu_se_hisat_gene)
plot_nonzero(hu_se_hisat_gene)

plot_libsize(hu_se_hisat_gene_mrna)
plot_libsize(hu_se_hisat_gene_rz)
```

# Normalize

```{r}
hu_sesn <- normalize(hu_se_salmon, transform = "log2", convert = "cpm",
                     filter = TRUE, norm = "quant")
plot_corheat(hu_sesn)
hu_sesn_pca <- plot_pca(hu_sesn)

pp(file = "images/hu_pca_sampletype.png")
hu_sesn_pca$plot
dev.off()
hu_sesn_pca

hu_detected <- subset_se(hu_se_salmon, subset = "detectionparasiteby7sl!='unknown'") %>%
  set_conditions(fact = "detectionparasiteby7sl") %>%
  set_batches("sample_type")
hu_detect_nb <- normalize(hu_detected, transform = "log2", convert = "cpm",
                          filter = TRUE, batch = "svaseq")
hu_detect_pca <- plot_pca(hu_detect_nb)
pp(file = "images/hu_pca_detect_sva.png")
hu_detect_pca$plot
dev.off()
hu_detect_pca
```

# Compare distribution of RZ/Stranded libraries

Maria Adelaida is interested in the distribution of the relatively few
rz samples vs the relatively large number of stranded mRNA libraries.

I think it is likely that the nasal samples are of primary interest.

```{r}
salmon_mrna_7sl <- set_conditions(hu_se_salmon_mrna, fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
salmon_mrna_7sl_norm <- normalize(salmon_mrna_7sl, convert = "cpm", filter = TRUE,
                                  norm = "quant", transform = "log2")
## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(salmon_mrna_7sl_norm)
salmon_mrna_7sl_nb <- normalize(salmon_mrna_7sl, convert = "cpm", filter = TRUE,
                                batch = "sva", transform = "log2")
plot_pca(salmon_mrna_7sl_nb)

hisat_mrna_7sl <- set_conditions(hu_se_hisat_gene_mrna, fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
hisat_mrna_7sl_norm <- normalize(hisat_mrna_7sl, convert = "cpm", filter = TRUE,
                                  norm = "quant", transform = "log2")
## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(hisat_mrna_7sl_norm)
hisat_mrna_7sl_nb <- normalize(hisat_mrna_7sl, convert = "cpm", filter = TRUE,
                                batch = "sva", transform = "log2")
plot_pca(hisat_mrna_7sl_nb)
```

Now restrict to just the nasal samples.

```{r}
salmon_nasal_mrna <- subset_se(hu_se_salmon_mrna, subset = "sample_type=='nasal swab'") %>%
  set_conditions(fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
salmon_nasal_mrna_norm <- normalize(salmon_nasal_mrna, convert = "cpm", filter = TRUE,
                                    norm = "quant", transform = "log2")
plot_pca(salmon_nasal_mrna_norm)
salmon_nasal_mrna_nb <- normalize(salmon_nasal_mrna, convert = "cpm", filter = TRUE,
                                  batch = "sva", transform = "log2")
plot_pca(salmon_nasal_mrna_nb)

hisat_nasal_mrna <- subset_se(hu_se_hisat_gene_mrna, subset = "sample_type=='nasal swab'") %>%
  set_conditions(fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
hisat_nasal_mrna_norm <- normalize(hisat_nasal_mrna, convert = "cpm", filter = TRUE,
                                    norm = "quant", transform = "log2")
plot_pca(hisat_nasal_mrna_norm)
hisat_nasal_mrna_nb <- normalize(hisat_nasal_mrna, convert = "cpm", filter = TRUE,
                                  batch = "sva", transform = "log2")
plot_pca(hisat_nasal_mrna_nb)
```

## Repeat with the ribo zero samples

```{r}
salmon_rz_7sl <- set_conditions(hu_se_salmon_rz, fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
salmon_rz_7sl_norm <- normalize(salmon_rz_7sl, convert = "cpm", filter = TRUE,
                                norm = "quant", transform = "log2")
## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(salmon_rz_7sl_norm)
salmon_rz_7sl_nb <- normalize(salmon_rz_7sl, convert = "cpm", filter = TRUE,
                              batch = "sva", transform = "log2")
plot_pca(salmon_rz_7sl_nb)

hisat_rz_7sl <- set_conditions(hu_se_hisat_gene_rz, fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
hisat_rz_7sl_norm <- normalize(hisat_rz_7sl, convert = "cpm", filter = TRUE,
                               norm = "quant", transform = "log2")
## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(hisat_rz_7sl_norm)
hisat_rz_7sl_nb <- normalize(hisat_rz_7sl, convert = "cpm", filter = TRUE,
                             batch = "sva", transform = "log2")
plot_pca(hisat_rz_7sl_nb)
```

Now restrict to just the nasal samples.

```{r}
salmon_nasal_rz <- subset_se(hu_se_salmon_rz, subset = "sample_type=='nasal swab'") %>%
  set_conditions(fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
salmon_nasal_rz_norm <- normalize(salmon_nasal_rz, convert = "cpm", filter = TRUE,
                                    norm = "quant", transform = "log2")
plot_pca(salmon_nasal_rz_norm)
salmon_nasal_rz_nb <- normalize(salmon_nasal_rz, convert = "cpm", filter = TRUE,
                                  batch = "sva", transform = "log2")
plot_pca(salmon_nasal_rz_nb)

hisat_nasal_rz <- subset_se(hu_se_hisat_gene_rz, subset = "sample_type=='nasal swab'") %>%
  set_conditions(fact = "detectionparasiteby7sl") %>%
  subset_se(subset = "condition!='notapplicable'")
hisat_nasal_rz_norm <- normalize(hisat_nasal_rz, convert = "cpm", filter = TRUE,
                                    norm = "quant", transform = "log2")
plot_pca(hisat_nasal_rz_norm)
hisat_nasal_rz_nb <- normalize(hisat_nasal_rz, convert = "cpm", filter = TRUE,
                                  batch = "sva", transform = "log2")
plot_pca(hisat_nasal_rz_nb)
```

# Look at sample type and 7sl

```{r}
hu_s7sl <- set_conditions(hu_se_salmon_mrna, fact = "sample_7sl")

hu_nasal <- subset_se(hu_s7sl, subset = "sample_type=='nasal swab'")
hu_nasal_nb <- normalize(hu_nasal, transform = "log2", convert = "cpm",
                          batch = "svaseq", filter = TRUE)
pp(file = "images/nasal_sample_np.png")
plot_pca(hu_nasal_nb)
dev.off()

hu_wbc <- subset_se(hu_s7sl, subset = "sample_type=='WBCs'")
hu_wbc_nb <- normalize(hu_wbc, transform = "log2", convert = "cpm",
                       batch = "svaseq", filter = TRUE)
pp(file = "images/wbc_sample_np.png")
plot_pca(hu_wbc_nb)
dev.off()
```

```{r}
short_factor <- gsub(x = as.character(colData(hu_nasal)[["condition"]]), pattern = ".*_(.*)$", replacement = "\\1")
hu_nasal <- set_conditions(hu_nasal, fact = as.factor(short_factor))
hu_nasal_np <- subset_se(hu_nasal, subset = "condition!='notapplicable'")

hu_nasal_de <- all_pairwise(hu_nasal_np, filter = TRUE, force = TRUE,
                            model_fstring = "~ 0 + condition", model_svs = "svaseq")
hu_nasal_de

hu_nasal_table <- combine_de_tables(hu_nasal_de, excel = "excel/persist_table.xlsx")
hu_nasal_table

hu_nasal_sig <- extract_significant_genes(hu_nasal_table, excel = "excel/persist_sig.xlsx")
hu_nasal_sig
```

# Healthy vs Scar samples

One query from our last meeting which I forgot about until I reread my
TODO notes: compare the samples marked as healthy compared to those
marked as scar.  These are two distantly separate skin biopsies of the
same person.

```{r}
hu_hs_de <- all_pairwise(hu_hs, filter = TRUE, force = TRUE,
                         model_svs = "svaseq", model_fstring = "~ 0 + condition")
hu_hs_table <- combine_de_tables(hu_hs_de, excel = "excel/healthy_vs_scar_table.xlsx")
hu_hs_table
hu_hs_sig <- extract_significant_genes(hu_hs_table, excel = "excel/healthy_vs_scar_sig.xlsx")
hu_hs_sig
```

# Take a peek at the kraken results

```{r}
hu_kraken_viral <- create_se(pre_meta[["new_meta"]], file_column = "kraken_matrix_viral",
                       handle_na = "zero")
hu_kraken_viral <- set_conditions(hu_kraken_viral, fact = "sample_type") %>%
  set_batches("detectionparasiteby7sl")

kraken_viral_norm <- normalize(hu_kraken_viral, filter = TRUE, norm = "cpm", transform = "log2")
plot_corheat(kraken_viral_norm)
plot_disheat(kraken_viral_norm)
plot_pca(kraken_viral_norm)

nasal_kraken <- subset_se(hu_kraken_viral, subset = "condition=='nasal swab'")
nasal_norm <- normalize(nasal_kraken_viral, filter = TRUE, norm = "cpm", transform = "log2")
plot_corheat(nasal_norm)


hu_kraken_bacteria <- create_se(pre_meta[["new_meta"]], file_column = "kraken_matrix_bacterial",
                       handle_na = "zero")
hu_kraken_bacteria <- set_conditions(hu_kraken_bacteria, fact = "sample_type") %>%
  set_batches("detectionparasiteby7sl")
colData(hu_kraken_bacteria)[["kraken_bacteria"]] <- kraken_bacteria

kraken_bacteria_norm <- normalize(hu_kraken_bacteria, filter = TRUE, norm = "cpm", transform = "log2")
plot_corheat(kraken_bacteria_norm)
plot_disheat(kraken_bacteria_norm)
plot_pca(kraken_bacteria_norm)
```

# Nasal as a proxy for everything else

In the beginning of this document, I created a peculiar factor out of
the nasal sample 7SL state and applied its result to every other
sample for each person; thus a person who was positive for the nasal
sample was deemed positive for everything.  Let us see what that looks
like...

```{r}
nasal_7sl_se <- set_conditions(hu_se_salmon, fact = "nasal_7sl_status")
nasal_7sl_hisat_se <- set_conditions(hu_se_hisat_genes, fact = "nasal_7sl_status")

nasal_7sl_se_nb <- normalize(nasal_7sl_se, transform = "log2", convert = "cpm", filter = TRUE,
                             batch = "svaseq")
plot_pca(nasal_7sl_se_nb)

nasal_7sl_de <- all_pairwise(nasal_7sl_se, filter = TRUE,
                             model_svs = "svaseq", model_fstring = "~ 0 + condition")
nasal_7sl_de
nasal_7sl_hisat_de <- all_pairwise(nasal_7sl_hisat_se, filter = TRUE,
                                   model_svs = "svaseq", model_fstring = "~ 0 + condition")
nasal_7sl_hisat_de


nasal_7sl_table <- combine_de_tables(nasal_7sl_de, excel = "excel/nasal_7sl_proxy_table.xlsx")
nasal_7sl_table
nasal_7sl_hisat_table <- combine_de_tables(nasal_7sl_hisat_de, excel = "excel/nasal_7sl_proxy_table.xlsx")
nasal_7sl_hisat_table
```

Oh, Maria Adelaida was actually looking only for the PBMC samples.

```{r}
pbmc_nasal_7sl_se <- subset_se(hu_se_salmon, subset = "condition=='PBMCs'") %>%
  set_conditions(fact = "nasal_7sl_status")
pbmc_nasal_7sl_hisat_se <- subset_se(hu_se_hisat_gene, subset = "condition=='PBMCs'") %>%
  set_conditions(fact = "nasal_7sl_status")

pbmc_nasal_hisat_norm <- normalize(pbmc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
                                   norm = "quant", filter = TRUE)
plot_pca(pbmc_nasal_hisat_norm)

pbmc_nasal_hisat_nb <- normalize(pbmc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
                                 batch = "svaseq", filter = "simple")
plot_pca(pbmc_nasal_hisat_nb)

pbmc_nasal_7sl_de <- all_pairwise(pbmc_nasal_7sl_se, filter = "simple",
                                  model_svs = "svaseq", model_fstring = "~ 0 + condition")
pbmc_nasal_7sl_table <- combine_de_tables(pbmc_nasal_7sl_de, excel = "excel/pbmc_nasal_proxy.xlsx")
```

# TODO 202512

Repeat this nasal proxy test using each of the other cell types.

The factors of likely interest are: "wbcs" "nasal swab" ideally both
"skin biopsy healthy" and "skin biopsy scar" but perhaps only "skin
biopsy".

```{r}
wbc_nasal_7sl_se <- subset_se(hu_se_salmon, subset = "condition=='WBCs'") %>%
  set_conditions(fact = "nasal_7sl_status")
wbc_nasal_7sl_hisat_se <- subset_se(hu_se_hisat_gene, subset = "condition=='WBCs'") %>%
  set_conditions(fact = "nasal_7sl_status")

wbc_nasal_hisat_norm <- normalize(wbc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
                                  filter = "simple", norm = "quant")
plot_pca(wbc_nasal_hisat_norm)
wbc_nasal_hisat_nb <- normalize(wbc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
                                  filter = "simple", batch = "svaseq")
plot_pca(wbc_nasal_hisat_nb)

wbc_nasal_7sl_de <- all_pairwise(wbc_nasal_7sl_se, filter = "simple",
                                  model_svs = "svaseq", model_fstring = "~ 0 + condition")
wbc_nasal_7sl_table <- combine_de_tables(wbc_nasal_7sl_de, excel = "excel/wbc_nasal_proxy.xlsx")
```
