There are a few methods of importing annotation data into R. I will attempt some of them in preparation for loading them into the S.cerevisiae RNASeq data.
AnnotationHub is a newer service and has promise to be an excellent top-level resource for gathering annotation data.
tmp <- sm(library(AnnotationHub))
ah = sm(AnnotationHub())
orgdbs <- sm(query(ah, "OrgDb"))
sc_orgdb <- sm(query(ah, c("OrgDB", "Saccharomyces"))) ## AH49589 | org.Sc.sgd.db.sqlite
sc_orgdb
## AnnotationHub with 7 records
## # snapshotDate(): 2017-10-27
## # $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
## # $species: Saccharomyces cerevisiae, Saccharomyces eubayanus, Schizosa...
## # $rdataclass: OrgDb
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## # tags, rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH57980"]]'
##
## title
## AH57980 | org.Sc.sgd.db.sqlite
## AH59735 | org.Schizosaccharomyces_pombe.eg.sqlite
## AH59859 | org.Saccharomyces_eubayanus.eg.sqlite
## AH59874 | org.Schizosaccharomyces_cryophilus_OY26.eg.sqlite
## AH59893 | org.Schizosaccharomyces_octosporus_yFS286.eg.sqlite
## AH59899 | org.Zygosaccharomyces_rouxii.eg.sqlite
## AH59913 | org.Schizosaccharomyces_japonicus_yFS275.eg.sqlite
sc_orgdb <- ah[["AH57980"]]
## loading from cache '/home/trey//.AnnotationHub/64726'
## Loading required package: AnnotationDbi
## Loading required package: stats4
## 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:AnnotationHub':
##
## cache
## Loading required package: IRanges
## Loading required package: S4Vectors
##
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:base':
##
## expand.grid
sc_orgdb
## OrgDb object:
## | DBSCHEMAVERSION: 2.1
## | Db type: OrgDb
## | Supporting package: AnnotationDbi
## | DBSCHEMA: YEAST_DB
## | ORGANISM: Saccharomyces cerevisiae
## | SPECIES: Yeast
## | YGSOURCENAME: Yeast Genome
## | YGSOURCEURL: http://downloads.yeastgenome.org/
## | YGSOURCEDATE: 14-Jan-2017
## | CENTRALID: ORF
## | TAXID: 559292
## | KEGGSOURCENAME: KEGG GENOME
## | KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
## | KEGGSOURCEDATE: 2011-Mar15
## | GOSOURCENAME: Gene Ontology
## | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
## | GOSOURCEDATE: 2017-Nov01
## | EGSOURCEDATE: 2017-Nov6
## | EGSOURCENAME: Entrez Gene
## | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
## | ENSOURCEDATE: 2017-Aug23
## | ENSOURCENAME: Ensembl
## | ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
## | UPSOURCENAME: Uniprot
## | UPSOURCEURL: http://www.UniProt.org/
## | UPSOURCEDATE: Tue Nov 7 21:11:11 2017
##
## Please see: help('select') for usage information
## Holy crap it worked!
sc_annotv1 <- load_orgdb_annotations(
sc_orgdb,
fields=c("alias", "description", "entrezid", "genename", "sgd"))
## Unable to find TYPE in the db, removing it.
## Unable to find CHR in the db, removing it.
## Unable to find TXSTRAND in the db, removing it.
## Unable to find TXSTART in the db, removing it.
## Unable to find TXEND in the db, removing it.
## Extracted all gene ids.
## 'select()' returned 1:many mapping between keys and columns
sc_annotv1 <- sc_annotv1[["genes"]]
tt <- please_install("TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")
tmp <- sm(library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene))
sc_txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
There is a non-zero chance we will want to use the actual genome sequence along with these annotations. The BSGenome packages provide that functionality.
tt <- sm(please_install("BSgenome.Scerevisiae.UCSC.sacCer3"))
A completely separate and competing annotation source is biomart.
sc_annotv2 <- sm(load_biomart_annotations("scerevisiae"))
sc_annotv2 <- sc_annotv2[["annotation"]]
head(sc_annotv2)
## transcriptID geneID
## X15S_rRNA 15S_rRNA 15S_rRNA
## X21S_rRNA 21S_rRNA 21S_rRNA
## HRA1 HRA1 HRA1
## ICR1 ICR1 ICR1
## LSR1 LSR1 LSR1
## NME1 NME1 NME1
## Description
## X15S_rRNA Ribosomal RNA of the small mitochondrial ribosomal subunit; MSU1 allele suppresses ochre stop mutations in mitochondrial protein-coding genes [Source:SGD;Acc:S000007287]
## X21S_rRNA Mitochondrial 21S rRNA; intron encodes the I-SceI DNA endonuclease [Source:SGD;Acc:S000007288]
## HRA1 Non-protein-coding RNA; substrate of RNase P, possibly involved in rRNA processing, specifically maturation of 20S precursor into the mature 18S rRNA [Source:SGD;Acc:S000119380]
## ICR1 Long intergenic regulatory ncRNA; has a key role in regulating transcription of the nearby protein-coding ORF FLO11; initiated far upstream from FLO11 and transcribed across much of the large promoter of FLO11, repressing FLO11 transcription in cis [Source:SGD;Acc:S000132612]
## LSR1 U2 spliceosomal RNA (U2 snRNA), component of the spliceosome; pairs with the branchpoint sequence; functionally equivalent to mammalian U2 snRNA; stress-induced pseudouridylations at positions 56 and 93 may contribute to regulation of splicing [Source:SGD;Acc:S000006478]
## NME1 RNA component of RNase MRP; RNase MRP cleaves pre-rRNA and has a role in cell cycle-regulated degradation of daughter cell-specific mRNAs; human ortholog is implicated in cartilage-hair hypoplasia (CHH) [Source:SGD;Acc:S000007436]
## Type length chromosome strand start end
## X15S_rRNA rRNA NA Mito 1 6546 8194
## X21S_rRNA rRNA NA Mito 1 58009 62447
## HRA1 ncRNA NA I 1 99305 99868
## ICR1 ncRNA NA IX -1 393884 397082
## LSR1 snRNA NA II -1 680688 681862
## NME1 snoRNA NA XIV 1 585587 585926
sc_ontology <- sm(load_biomart_go("scerevisiae"))
sc_ontology <- sc_ontology[["go"]]
head(sc_ontology)
## ID GO
## 1 YHR055C GO:0046872
## 2 YHR055C GO:0005829
## 3 YHR055C GO:0016209
## 4 YHR055C GO:0004784
## 5 YHR055C GO:0019430
## 6 YHR055C GO:0005507
In contrast, it is possible to load most annotations of interest directly from the gff files used in the alignments.
## The old way of getting genome/annotation data
sc_gff <- "reference/scerevisiae.gff.gz"
sc_gff_annotations <- load_gff_annotations(sc_gff, type="gene")
## Trying attempt: rtracklayer::import.gff3(gff, sequenceRegionsAsSeqinfo=TRUE)
## Trying attempt: rtracklayer::import.gff3(gff, sequenceRegionsAsSeqinfo=FALSE)
## Trying attempt: rtracklayer::import.gff2(gff, sequenceRegionsAsSeqinfo=TRUE)
## Had a successful gff import with rtracklayer::import.gff2(gff, sequenceRegionsAsSeqinfo=TRUE)
## Returning a df with 18 columns and 7050 rows.
rownames(sc_gff_annotations) <- make.names(sc_gff_annotations$transcript_name, unique=TRUE)
head(sc_gff_annotations)
## seqnames start end width strand source type score
## YAL069W I 335 646 312 + protein_coding gene NA
## YAL068W.A I 538 789 252 + protein_coding gene NA
## PAU8 I 1810 2169 360 - protein_coding gene NA
## YAL067W.A I 2480 2704 225 + protein_coding gene NA
## SEO1 I 7238 9016 1779 - protein_coding gene NA
## YAL066W I 10091 10396 306 + protein_coding gene NA
## phase exon_number gene_id ID p_id protein_id
## YAL069W 0 1 YAL069W YAL069W P3633 YAL069W
## YAL068W.A 0 1 YAL068W-A YAL068W-A P5377 YAL068W-A
## PAU8 0 1 YAL068C PAU8 P6023 YAL068C
## YAL067W.A 0 1 YAL067W-A YAL067W-A P4547 YAL067W-A
## SEO1 0 1 YAL067C SEO1 P5747 YAL067C
## YAL066W 0 1 YAL066W YAL066W P1766 YAL066W
## transcript_id transcript_name tss_id seqedit
## YAL069W YAL069W YAL069W TSS1128 <NA>
## YAL068W.A YAL068W-A YAL068W-A TSS5439 <NA>
## PAU8 YAL068C PAU8 TSS249 <NA>
## YAL067W.A YAL067W-A YAL067W-A TSS1248 <NA>
## SEO1 YAL067C SEO1 TSS5464 <NA>
## YAL066W YAL066W YAL066W TSS2674 <NA>
In the following block we create an expressionset using the sample sheet and the annotations.
Annoyingly, the gff annotations are keyed in a peculiar fashion. Therefore I need to do a little work to merge them.
## Start by making locations for the biomart data
sc_annotv2[["fwd_location"]] <- paste0(sc_annotv2[["chromosome"]], "_", sc_annotv2[["start"]])
sc_annotv2[["rev_location"]] <- paste0(sc_annotv2[["chromosome"]], "_", sc_annotv2[["end"]])
## Do the same for the gff annotations
sc_gff_annotations[["fwd_location"]] <- paste0(sc_gff_annotations[["seqnames"]], "_", sc_gff_annotations[["start"]])
sc_gff_annotations[["rev_location"]] <- paste0(sc_gff_annotations[["seqnames"]], "_", sc_gff_annotations[["end"]])
sc_gff_annotations[["gff_rowname"]] <- rownames(sc_gff_annotations)
## Now merge them.
sc_fwd_annotations <- merge(sc_annotv2, sc_gff_annotations, by="fwd_location")
sc_rev_annotations <- merge(sc_annotv2, sc_gff_annotations, by="rev_location")
colnames(sc_fwd_annotations) <- c("location","transcriptID","geneID", "Description",
"Type", "length", "chromosome", "strand.x", "start.x",
"end.x", "location.x", "seqnames",
"start.y", "end.y", "width", "strand.y", "source", "type",
"score", "phase", "exon_number", "gene_id", "ID", "p_id",
"protein_id", "transcript_id", "transcript_name", "tss_id",
"seqedit", "location.y", "gff_rowname")
colnames(sc_rev_annotations) <- colnames(sc_fwd_annotations)
sc_all_annotations <- rbind(sc_fwd_annotations, sc_rev_annotations)
rownames(sc_all_annotations) <- make.names(sc_all_annotations[["gff_rowname"]], unique=TRUE)
sc_all_annotations <- sc_all_annotations[, c("transcriptID", "geneID", "Description", "Type",
"length", "chromosome", "strand.x", "start.x", "end.x",
"tss_id")]
colnames(sc_all_annotations) <- c("transcriptID", "geneID", "Description", "Type", "length",
"chromosome", "strand", "start", "end", "tss_id")
sc_all_annotations[["location"]] <- paste0(sc_all_annotations[["chromosome"]], "_", sc_all_annotations[["start"]], "_", sc_all_annotations[["end"]])
sc2_expt <- create_expt(
metadata="sample_sheets/all_samples.xlsx",
gene_info=sc_all_annotations,
file_column="bt2file")
## Reading the sample metadata.
## The sample definitions comprises: 28, 19 rows, columns.
## Reading count tables.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0774/outputs/bowtie2_scerevisiae/hpgl0774_forward-trimmed.count.xz contains 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0775/outputs/bowtie2_scerevisiae/hpgl0775_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0776/outputs/bowtie2_scerevisiae/hpgl0776_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0777/outputs/bowtie2_scerevisiae/hpgl0777_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0778/outputs/bowtie2_scerevisiae/hpgl0778_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0779/outputs/bowtie2_scerevisiae/hpgl0779_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0780/outputs/bowtie2_scerevisiae/hpgl0780_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0781/outputs/bowtie2_scerevisiae/hpgl0781_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0782/outputs/bowtie2_scerevisiae/hpgl0782_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0783/outputs/bowtie2_scerevisiae/hpgl0783_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0784/outputs/bowtie2_scerevisiae/hpgl0784_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0785/outputs/bowtie2_scerevisiae/hpgl0785_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0786/outputs/bowtie2_scerevisiae/hpgl0786_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0787/outputs/bowtie2_scerevisiae/hpgl0787_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0788/outputs/bowtie2_scerevisiae/hpgl0788_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5_2017/preprocessing/v2/hpgl0789/outputs/bowtie2_scerevisiae/hpgl0789_forward-trimmed.count.xz contains 7131 rows and merges to 7131 rows.
## Finished reading count tables.
## Matched 6540 annotations and counts.
## Bringing together the count matrix and gene information.
## Some annotations were lost in merging, setting them to 'undefined'.
knitr::kable(head(exprs(sc2_expt$expressionset)))
hpgl0774 | hpgl0775 | hpgl0776 | hpgl0777 | hpgl0778 | hpgl0779 | hpgl0780 | hpgl0781 | hpgl0782 | hpgl0783 | hpgl0784 | hpgl0785 | hpgl0786 | hpgl0787 | hpgl0788 | hpgl0789 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
X15S_rRNA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
X21S_rRNA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
AAC1 | 536 | 477 | 743 | 443 | 634 | 188 | 763 | 414 | 175 | 145 | 140 | 237 | 124 | 142 | 141 | 181 |
AAC3 | 126 | 216 | 93 | 765 | 152 | 154 | 102 | 738 | 295 | 119 | 341 | 542 | 210 | 118 | 438 | 1071 |
AAD10 | 1784 | 1928 | 2327 | 3869 | 2172 | 994 | 2472 | 3551 | 365 | 589 | 1476 | 1593 | 352 | 542 | 1782 | 2082 |
AAD14 | 1054 | 901 | 1222 | 1863 | 1106 | 836 | 1307 | 1588 | 542 | 766 | 1580 | 1814 | 439 | 795 | 1924 | 2333 |
knitr::kable(head(fData(sc2_expt$expressionset)))
transcriptID | geneID | Description | Type | length | chromosome | strand | start | end | tss_id | location | |
---|---|---|---|---|---|---|---|---|---|---|---|
X15S_rRNA | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined |
X21S_rRNA | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined | undefined |
AAC1 | YMR056C | YMR056C | Mitochondrial inner membrane ADP/ATP translocator; exchanges cytosolic ADP for mitochondrially synthesized ATP; phosphorylated; Aac1p is a minor isoform while Pet9p is the major ADP/ATP translocator; relocalizes from mitochondrion to cytoplasm upon DNA replication stress [Source:SGD;Acc:S000004660] | protein_coding | 930 | XIII | -1 | 387315 | 388244 | TSS5132 | XIII_387315_388244 |
AAC3 | YBR085W | YBR085W | Mitochondrial inner membrane ADP/ATP translocator; exchanges cytosolic ADP for mitochondrially synthesized ATP; expressed under anaerobic conditions; similar to Aac1p; has roles in maintenance of viability and in respiration; AAC3 has a paralog, PET9, that arose from the whole genome duplication [Source:SGD;Acc:S000000289] | protein_coding | 924 | II | 1 | 415983 | 416906 | TSS1609 | II_415983_416906 |
AAD10 | YJR155W | YJR155W | Putative aryl-alcohol dehydrogenase; similar to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role; members of the AAD gene family comprise three pairs (AAD3 + AAD15, AAD6/AAD16 + AAD4, AAD10 + AAD14) whose two genes are more related to one another than to other members of the family [Source:SGD;Acc:S000003916] | protein_coding | 867 | X | 1 | 727405 | 728271 | TSS5024 | X_727405_728271 |
AAD14 | YNL331C | YNL331C | Putative aryl-alcohol dehydrogenase; similar to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role; members of the AAD gene family comprise three pairs (AAD3 + AAD15, AAD6/AAD16 + AAD4, AAD10 + AAD14) whose two genes are more related to one another than to other members of the family [Source:SGD;Acc:S000005275] | protein_coding | 1131 | XIV | -1 | 16118 | 17248 | TSS6941 | XIV_16118_17248 |
knitr::kable(head(pData(sc2_expt$expressionset)))
sampleid | strain | condition | batch | originalbatch | tube | cbf5igv | upf1igv | incubationtime | genotype | conc | bttotalreads | bttotalmapped | btleftmapped | btrightmapped | bowtiefile | bt2file | intronfile | allfile | file | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
hpgl0774 | hpgl0774 | yJD1524 | WT | E2B1 | E2B1 | f | wt | wt | 18h | wt ade2-1 can1-100 his3-11 leu2-3, 112 trp1-1 ura3-1 cbf5::TRP1 + CBF5 on pRS313 | NA | NA | NA | NA | NA | NA | preprocessing/v2/hpgl0774/outputs/bowtie2_scerevisiae/hpgl0774_forward-trimmed.count.xz | preprocessing/v2/hpgl0774/outputs/bowtie2_scerevisiae/introns.count.xz | preprocessing/v2/hpgl0774/outputs/bowtie2_scerevisiae/hpgl0774_forward-trimmed.count.xz | null |
hpgl0775 | hpgl0775 | yJD1525 | cbf5_D95A | E2B1 | E2B1 | f | mut | wt | 18h | d95a ade2-1 can1-100 his3-11 leu2-3, 112 trp1-1 ura3-1 cbf5::TRP1 + CBF5 D95A on pRS313 | NA | NA | NA | NA | NA | NA | preprocessing/v2/hpgl0775/outputs/bowtie2_scerevisiae/hpgl0775_forward-trimmed.count.xz | preprocessing/v2/hpgl0775/outputs/bowtie2_scerevisiae/introns.count.xz | preprocessing/v2/hpgl0775/outputs/bowtie2_scerevisiae/hpgl0775_forward-trimmed.count.xz | null |
hpgl0776 | hpgl0776 | yJD1745 | upf1d | E2B1 | E2B1 | f | wt | mut | 18h | wt ade2-1 can1-100 his3-11 leu2-3, 112 trp1-1 ura3-1 cbf5::TRP1 upf1::LEU2 + CBF5 on pRS313 (yJD1524 upf1Δ) | NA | NA | NA | NA | NA | NA | preprocessing/v2/hpgl0776/outputs/bowtie2_scerevisiae/hpgl0776_forward-trimmed.count.xz | preprocessing/v2/hpgl0776/outputs/bowtie2_scerevisiae/introns.count.xz | preprocessing/v2/hpgl0776/outputs/bowtie2_scerevisiae/hpgl0776_forward-trimmed.count.xz | null |
hpgl0777 | hpgl0777 | yJD1746 | cbf5_D95A upf1d | E2B1 | E2B1 | f | mut | mut | 18h | d95a ade2-1 can1-100 his3-11 leu2-3, 112 trp1-1 ura3-1 cbf5::TRP1 upf1::LEU2 + CBF5 D95A on pRS313 (yJD1525 upf1Δ) | NA | NA | NA | NA | NA | NA | preprocessing/v2/hpgl0777/outputs/bowtie2_scerevisiae/hpgl0777_forward-trimmed.count.xz | preprocessing/v2/hpgl0777/outputs/bowtie2_scerevisiae/introns.count.xz | preprocessing/v2/hpgl0777/outputs/bowtie2_scerevisiae/hpgl0777_forward-trimmed.count.xz | null |
hpgl0778 | hpgl0778 | yJD1524 | WT | E2B1 | E2B2 | g | wt | wt | 18h | wt ade2-1 can1-100 his3-11 leu2-3, 112 trp1-1 ura3-1 cbf5::TRP1 + CBF5 on pRS313 | NA | NA | NA | NA | NA | NA | preprocessing/v2/hpgl0778/outputs/bowtie2_scerevisiae/hpgl0778_forward-trimmed.count.xz | preprocessing/v2/hpgl0778/outputs/bowtie2_scerevisiae/introns.count.xz | preprocessing/v2/hpgl0778/outputs/bowtie2_scerevisiae/hpgl0778_forward-trimmed.count.xz | null |
hpgl0779 | hpgl0779 | yJD1525 | cbf5_D95A | E2B1 | E2B2 | g | mut | wt | 18h | d95a ade2-1 can1-100 his3-11 leu2-3, 112 trp1-1 ura3-1 cbf5::TRP1 + CBF5 D95A on pRS313 | NA | NA | NA | NA | NA | NA | preprocessing/v2/hpgl0779/outputs/bowtie2_scerevisiae/hpgl0779_forward-trimmed.count.xz | preprocessing/v2/hpgl0779/outputs/bowtie2_scerevisiae/introns.count.xz | preprocessing/v2/hpgl0779/outputs/bowtie2_scerevisiae/hpgl0779_forward-trimmed.count.xz | null |
if (!isTRUE(get0("skip_load"))) {
pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
tmp <- sm(saveme(filename=this_save))
}
## If you wish to reproduce this exact build of hpgltools, invoke the following:
## > git clone http://github.com/abelew/hpgltools.git
## > git reset 5d8c266e48bb9f73cdac8300e5c7c9f5baf003dc
## R> packrat::restore()
## This is hpgltools commit: Wed Mar 21 15:55:32 2018 -0400: 5d8c266e48bb9f73cdac8300e5c7c9f5baf003dc