Mercurial > repos > iuc > deseq2

annotate get_deseq_dataset.R @ 17:d9e5cadc7f0b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
author iuc
date Wed, 05 Sep 2018 15:54:03 -0400
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children c56e0689e46e
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17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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1 get_deseq_dataset <- function(sampleTable, header, designFormula, tximport, txtype, tx2gene) {
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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2
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3 dir <- ""
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4
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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 }
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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10
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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 file is required for tximport")
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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13 if (tolower(file_ext(opt$tx2gene)) == "gtf") {
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14 gtfFile <-tx2gene
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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15 } else {
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16 gtfFile <- NULL
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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17 tx2gene <- read.table(tx2gene, header=FALSE)
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18 }
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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19 useTXI <- TRUE
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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20 } else {
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21 useTXI <- FALSE
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22 }
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23
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24 if (!useTXI & hasHeader) {
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25 countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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26 tbl <- do.call("cbind", countfiles)
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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27 colnames(tbl) <- rownames(sampleTable) # take sample ids from header
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28
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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",
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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31 "not_aligned", "alignment_not_unique")
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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32 specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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33 tbl <- tbl[!specialRows, , drop = FALSE]
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34
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35 dds <- DESeqDataSetFromMatrix(countData = tbl,
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36 colData = subset(sampleTable, select=-(filename)),
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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37 design = designFormula)
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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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
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 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 # first need to make the tx2gene table
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49 # this takes ~2-3 minutes using Bioconductor functions
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50 if (!is.null(gtfFile)) {
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51 suppressPackageStartupMessages({
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52 library("GenomicFeatures")
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53 })
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54 txdb <- makeTxDbFromGFF(gtfFile, format="gtf")
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55 k <- keys(txdb, keytype = "GENEID")
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56 df <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
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57 tx2gene <- df[, 2:1] # tx ID, then gene ID
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58 }
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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59 library("tximport")
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60 txiFiles <- as.character(sampleTable$filename)
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61 labs <- row.names(sampleTable)
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62 names(txiFiles) <- labs
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63 txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene)
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64 dds <- DESeqDataSetFromTximport(txi,
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65 subset(sampleTable, select=-c(filename)),
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66 designFormula)
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67 }
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68 return(dds)
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69 }