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")## Unable to perform useMart, perhaps the host/mart is incorrect: useast.ensembl.org ENSEMBL_MART_ENSEMBL.## Error in `req_perform()`:
## ! Failed to perform HTTP request.
## Caused by error in `curl::curl_fetch_memory()`:
## ! Could not resolve hostname [useast.ensembl.org]:
## Could not resolve host: useast.ensembl.orgpanamensis_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"
modified_meta[["nasal_7sl_status"]] <- as.factor(modified_meta[["nasal_7sl_status"]])
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.
## Error: object 'hs_annot' not found7 Quick peek at the SL samples, hg38 release 115
7.1 Gather the transcript and gene annotations.
## Error: object 'hs_annot' not found## Error: object 'hs_annot' not found7.2 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).## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hg_map' not foundhu_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).## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hg_genes' not found7.3 Figure out which samples do not have 7SL categories
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_salmon' not found## Error: object 'hu_se_salmon' not found## Error: object 'hu_se_hisat_gene' not foundsample_7sl <- paste0(colData(hu_se_salmon)[["sample_type"]], "_",
colData(hu_se_salmon)[["detectionparasiteby7sl"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_salmon' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'gsub': object 'sample_7sl' not found## Error: object 'sample_7sl' not found## Error: object 'sample_7sl' not found7.4 Healthy vs scar samples
healthy_vs_scar <- gsub(x = colData(hu_se_salmon)[["sample_type"]],
pattern = "^skin biopsy ", replacement = "")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'gsub': error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_salmon' not found## Error: object 'healthy_vs_scar' not found## Error: object 'healthy_vs_scar' not found7.5 Clean up missing 7SL detection samples
I think the last of these has been fixed since the last time I updated this sheet.
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'undef_7sl' not foundif (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.")
}## Error: object 'undef_7sl' not found7.6 Print current state
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene' not found7.7 Combine 7SL status and the sample type into one factor
sample_7sl <- paste0(colData(hu_se_hisat_gene)[["sample_type"]], "_",
colData(hu_se_hisat_gene)[["detectionparasiteby7sl"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene' not found## Error: object 'sample_7sl' not found## Error: object 'sample_7sl' not found7.8 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")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon' not foundhu_se_salmon_rz <- set_conditions(hu_se_salmon, fact = "sample_type") %>%
subset_se(subset = "library_type=='RZ'") %>%
set_batches("detectionparasiteby7sl")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon' not foundhu_se_hisat_gene_mrna <- set_conditions(hu_se_hisat_gene, fact = "sample_type") %>%
subset_se(subset = "library_type=='mRNA'") %>%
set_batches("detectionparasiteby7sl")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene' not foundhu_se_hisat_gene_rz <- set_conditions(hu_se_hisat_gene, fact = "sample_type") %>%
subset_se(subset = "library_type=='RZ'") %>%
set_batches("detectionparasiteby7sl")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene' not found7.9 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")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon' not foundhu_hs_hisat_mrna <- subset_se(hu_se_hisat_gene_mrna, subset = "hs=='healthy'|hs=='scar'") %>%
set_conditions(fact = "hs")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene_mrna' not found8 HU Metadata
hu_mapped_mrna <- plot_metadata_factors(hu_se_hisat_gene_mrna, column = "hisat_genome_percent_log_hg38_115")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene_mrna' not found## Error: object 'hu_mapped_mrna' not foundhu_mapped_rz <- plot_metadata_factors(hu_se_hisat_gene_rz, column = "hisat_genome_percent_log_hg38_115")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene_rz' not found## Error: object 'hu_mapped_rz' not foundhu_observed_mrna <- plot_metadata_factors(hu_se_hisat_gene_mrna, column = "salmon_observed_genes_hg38_115")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene_mrna' not found## Error: object 'hu_observed_mrna' not foundhu_observed_rz <- plot_metadata_factors(hu_se_hisat_gene_rz, column = "salmon_observed_genes_hg38_115")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_hisat_gene_rz' not found## Error: object 'hu_observed_rz' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_salmon_mrna' not found## Error: object 'hu_pct_mrna' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_se_salmon_rz' not found## Error: object 'hu_pct_rz' not foundhu_sankey <- plot_meta_sankey(hu_se_salmon, factors = c("detectionparasiteby7sl", "sample_type", "library_type"))## Error in h(simpleError(msg, call)): error in evaluating the argument 'design' in selecting a method for function 'plot_meta_sankey': object 'hu_se_salmon' not found## Error: object 'hu_sankey' not found9 nonzero/libsize/etc
## Error: object 'hu_se_salmon' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_libsize': object 'hu_se_salmon' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_nonzero': object 'hu_se_salmon' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_libsize': object 'hu_se_hisat_gene' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_nonzero': object 'hu_se_hisat_gene' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_libsize': object 'hu_se_hisat_gene_mrna' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_libsize': object 'hu_se_hisat_gene_rz' not found10 Normalize
hu_sesn <- normalize(hu_se_salmon, transform = "log2", convert = "cpm",
filter = TRUE, norm = "quant")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hu_se_salmon' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'input_data' in selecting a method for function 'plot_heatmap': object 'hu_sesn' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hu_sesn' not found## Error: object 'hu_sesn_pca' not found## png
## 2## Error: object 'hu_sesn_pca' not foundhu_detected <- subset_se(hu_se_salmon, subset = "detectionparasiteby7sl!='unknown'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
set_batches("sample_type")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon' not foundhu_detect_nb <- normalize(hu_detected, transform = "log2", convert = "cpm",
filter = TRUE, batch = "svaseq")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hu_detected' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hu_detect_nb' not found## Error: object 'hu_detect_pca' not found## png
## 2## Error: object 'hu_detect_pca' not found11 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'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon_mrna' not foundsalmon_mrna_7sl_norm <- normalize(salmon_mrna_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_mrna_7sl' not found## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(salmon_mrna_7sl_norm)## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_mrna_7sl_norm' not foundsalmon_mrna_7sl_nb <- normalize(salmon_mrna_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_mrna_7sl' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_mrna_7sl_nb' not foundhisat_mrna_7sl <- set_conditions(hu_se_hisat_gene_mrna, fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene_mrna' not foundhisat_mrna_7sl_norm <- normalize(hisat_mrna_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_mrna_7sl' not found## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(hisat_mrna_7sl_norm)## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_mrna_7sl_norm' not foundhisat_mrna_7sl_nb <- normalize(hisat_mrna_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_mrna_7sl' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_mrna_7sl_nb' not foundNow 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'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon_mrna' not foundsalmon_nasal_mrna_norm <- normalize(salmon_nasal_mrna, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_nasal_mrna' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_nasal_mrna_norm' not foundsalmon_nasal_mrna_nb <- normalize(salmon_nasal_mrna, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_nasal_mrna' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_nasal_mrna_nb' not foundhisat_nasal_mrna <- subset_se(hu_se_hisat_gene_mrna, subset = "sample_type=='nasal swab'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene_mrna' not foundhisat_nasal_mrna_norm <- normalize(hisat_nasal_mrna, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_nasal_mrna' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_nasal_mrna_norm' not foundhisat_nasal_mrna_nb <- normalize(hisat_nasal_mrna, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_nasal_mrna' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_nasal_mrna_nb' not found11.1 Repeat with the ribo zero samples
salmon_rz_7sl <- set_conditions(hu_se_salmon_rz, fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon_rz' not foundsalmon_rz_7sl_norm <- normalize(salmon_rz_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_rz_7sl' not found## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(salmon_rz_7sl_norm)## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_rz_7sl_norm' not foundsalmon_rz_7sl_nb <- normalize(salmon_rz_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_rz_7sl' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_rz_7sl_nb' not foundhisat_rz_7sl <- set_conditions(hu_se_hisat_gene_rz, fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene_rz' not foundhisat_rz_7sl_norm <- normalize(hisat_rz_7sl, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_rz_7sl' not found## This still clusters primarily by sample type, and there are precious few positive samples.
plot_pca(hisat_rz_7sl_norm)## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_rz_7sl_norm' not foundhisat_rz_7sl_nb <- normalize(hisat_rz_7sl, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_rz_7sl' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_rz_7sl_nb' not foundNow 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'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon_rz' not foundsalmon_nasal_rz_norm <- normalize(salmon_nasal_rz, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_nasal_rz' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_nasal_rz_norm' not foundsalmon_nasal_rz_nb <- normalize(salmon_nasal_rz, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'salmon_nasal_rz' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'salmon_nasal_rz_nb' not foundhisat_nasal_rz <- subset_se(hu_se_hisat_gene_rz, subset = "sample_type=='nasal swab'") %>%
set_conditions(fact = "detectionparasiteby7sl") %>%
subset_se(subset = "condition!='notapplicable'")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene_rz' not foundhisat_nasal_rz_norm <- normalize(hisat_nasal_rz, convert = "cpm", filter = TRUE,
norm = "quant", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_nasal_rz' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_nasal_rz_norm' not foundhisat_nasal_rz_nb <- normalize(hisat_nasal_rz, convert = "cpm", filter = TRUE,
batch = "sva", transform = "log2")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hisat_nasal_rz' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hisat_nasal_rz_nb' not found12 Look at sample type and 7sl
## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon_mrna' not found## Error: object 'hu_s7sl' not foundhu_nasal_nb <- normalize(hu_nasal, transform = "log2", convert = "cpm",
batch = "svaseq", filter = TRUE)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hu_nasal' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hu_nasal_nb' not found## png
## 2## Error: object 'hu_s7sl' not foundhu_wbc_nb <- normalize(hu_wbc, transform = "log2", convert = "cpm",
batch = "svaseq", filter = TRUE)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'hu_wbc' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'hu_wbc_nb' not found## png
## 2short_factor <- gsub(x = as.character(colData(hu_nasal)[["condition"]]), pattern = ".*_(.*)$", replacement = "\\1")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'gsub': error in evaluating the argument 'x' in selecting a method for function 'colData': object 'hu_nasal' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_nasal' not found## Error: object 'hu_nasal' not foundhu_nasal_de <- all_pairwise(hu_nasal_np, filter = TRUE, force = TRUE,
model_fstring = "~ 0 + condition", model_svs = "svaseq")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'hu_nasal_np' not found## Error: object 'hu_nasal_de' not found## Deleting the file excel/persist_table.xlsx before writing the tables.## Error: object 'hu_nasal_de' not found## Error: object 'hu_nasal_table' not found## Deleting the file excel/persist_sig.xlsx before writing the tables.## Error: object 'hu_nasal_table' not found## Error: object 'hu_nasal_sig' not found13 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_hisat_mrna, 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_hisat_mrna' not found## Error: object 'hu_hs_de' not found## Error: object 'hu_hs_table' not found## 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_viral <- subset_se(hu_kraken_viral, subset = "condition=='nasal swab'")
nasal_norm <- normalize(nasal_kraken_viral, filter = TRUE, norm = "cpm", transform = "log2")## 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 8804 values equal to 0, adding 1 to the matrix.## A heatmap of pairwise sample correlations ranging from:
## 0.765126924228018 to 0.959000311538253.
hu_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:
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## /z1/scratch/atb/rnaseq/lpanamensis_persistence_2023/preprocessing/PRHU0091/outputs/20250918kraken_bacteria/kraken_report_matrix.tsv has
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## 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 29kraken_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…
## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon' not found## 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")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'nasal_7sl_se' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'nasal_7sl_se_nb' not foundnasal_7sl_de <- all_pairwise(nasal_7sl_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_se' not found## Error: object 'nasal_7sl_de' not foundnasal_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## Error: object 'nasal_7sl_de' not found## Error: object 'nasal_7sl_table' not foundnasal_7sl_hisat_table <- combine_de_tables(nasal_7sl_hisat_de, excel = "excel/nasal_7sl_proxy_table.xlsx")## 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")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon' not foundpbmc_nasal_7sl_hisat_se <- subset_se(hu_se_hisat_gene, subset = "condition=='PBMCs'") %>%
set_conditions(fact = "nasal_7sl_status")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene' not foundpbmc_nasal_hisat_norm <- normalize(pbmc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
norm = "quant", filter = TRUE)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'pbmc_nasal_7sl_hisat_se' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'pbmc_nasal_hisat_norm' not foundpbmc_nasal_hisat_nb <- normalize(pbmc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
batch = "svaseq", filter = "simple")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'pbmc_nasal_7sl_hisat_se' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'pbmc_nasal_hisat_nb' not foundpbmc_nasal_7sl_de <- all_pairwise(pbmc_nasal_7sl_se, filter = "simple",
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 'pbmc_nasal_7sl_se' not found## Deleting the file excel/pbmc_nasal_proxy.xlsx before writing the tables.## Error: object 'pbmc_nasal_7sl_de' not found16 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")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_salmon' not foundwbc_nasal_7sl_hisat_se <- subset_se(hu_se_hisat_gene, subset = "condition=='WBCs'") %>%
set_conditions(fact = "nasal_7sl_status")## Error in h(simpleError(msg, call)): error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'hu_se_hisat_gene' not foundwbc_nasal_hisat_norm <- normalize(wbc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
filter = "simple", norm = "quant")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'wbc_nasal_7sl_hisat_se' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'wbc_nasal_hisat_norm' not foundwbc_nasal_hisat_nb <- normalize(wbc_nasal_7sl_hisat_se, transform = "log2", convert = "cpm",
filter = "simple", batch = "svaseq")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'wbc_nasal_7sl_hisat_se' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'wbc_nasal_hisat_nb' not foundwbc_nasal_7sl_de <- all_pairwise(wbc_nasal_7sl_se, filter = "simple",
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 'wbc_nasal_7sl_se' not found## Deleting the file excel/wbc_nasal_proxy.xlsx before writing the tables.## Error: object 'wbc_nasal_7sl_de' not 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