Mercurial > repos > iuc > ruvseq

annotate get_deseq_dataset.R @ 1:c24765926774 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
author iuc
date Tue, 26 Mar 2019 06:25:38 -0400
parents 61dffb20b6f9
children fed9d0350d72
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61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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1 get_deseq_dataset <- function(sampleTable, header, designFormula, tximport, txtype, tx2gene) {
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3 dir <- ""
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5 if (!is.null(header)) {
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6 hasHeader <- TRUE
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7 } else {
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8 hasHeader <- FALSE
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9 }
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11 if (!is.null(tximport)) {
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12 if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport")
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13 if (tolower(file_ext(tx2gene)) == "gff") {
c24765926774 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
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14 gffFile <-tx2gene
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15 } else {
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c24765926774 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
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16 gffFile <- NULL
c24765926774 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
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17 tx2gene <- read.table(tx2gene, header=hasHeader)
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18 }
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19 useTXI <- TRUE
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20 } else {
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21 useTXI <- FALSE
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22 }
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24 if (!useTXI & hasHeader) {
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25 countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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26 tbl <- do.call("cbind", countfiles)
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27 colnames(tbl) <- rownames(sampleTable) # take sample ids from header
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29 # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
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30 oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual",
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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31 "not_aligned", "alignment_not_unique")
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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32 specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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33 tbl <- tbl[!specialRows, , drop = FALSE]
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35 dds <- DESeqDataSetFromMatrix(countData = tbl,
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36 colData = subset(sampleTable, select=-(filename)),
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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37 design = designFormula)
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38 } else if (!useTXI & !hasHeader) {
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39
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40 # construct the object from HTSeq files
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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41 dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
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42 directory = dir,
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43 design = designFormula)
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44 colnames(dds) <- row.names(sampleTable)
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45
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46 } else {
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47 # construct the object using tximport
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48 library("tximport")
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49 txiFiles <- as.character(sampleTable$filename)
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50 labs <- row.names(sampleTable)
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51 names(txiFiles) <- labs
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52 if (!is.null(gffFile)) {
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53 # first need to make the tx2gene table
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54 # this takes ~2-3 minutes using Bioconductor functions
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55 suppressPackageStartupMessages({
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56 library("GenomicFeatures")
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57 })
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58 txdb <- makeTxDbFromGFF(gffFile)
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59 k <- keys(txdb, keytype = "TXNAME")
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60 tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME")
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61 # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name)
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62 tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME)
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63 }
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64 try(txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene))
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65 if (!exists("txi")) {
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66 # Remove version from transcript IDs in tx2gene...
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67 tx2gene$TXNAME <- sub('\\.[0-9]+$', '', tx2gene$TXNAME)
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68 # ...and in txiFiles
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69 txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene, ignoreTxVersion=TRUE)
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70 }
0
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71 dds <- DESeqDataSetFromTximport(txi,
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72 subset(sampleTable, select=-c(filename)),
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73 designFormula)
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74 }
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75 return(dds)
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76 }