annotate get_deseq_dataset.R @ 24:71bacea10eee draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"

get_deseq_dataset <- function(sampleTable, header, designFormula, tximport, txtype, tx2gene) {

  dir <- ""

  if (!is.null(header)) {
    hasHeader <- TRUE
  } else {
    hasHeader <- FALSE
  }

  if (!is.null(tximport)) {
    if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport")
    if (tolower(file_ext(tx2gene)) == "gff") {
      gffFile <-tx2gene
    } else {
      gffFile <- NULL
      tx2gene <- read.table(tx2gene, header=hasHeader)
    }
    useTXI <- TRUE
  } else {
    useTXI <- FALSE
  }

  if (!useTXI & hasHeader) {
      countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
      tbl <- do.call("cbind", countfiles)
      colnames(tbl) <- rownames(sampleTable) # take sample ids from header

      # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
      oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual",
          "not_aligned", "alignment_not_unique")
      specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames
      tbl <- tbl[!specialRows, , drop = FALSE]

      dds <- DESeqDataSetFromMatrix(countData = tbl,
                                    colData = subset(sampleTable, select=-(filename)),
                                    design = designFormula)
  } else if (!useTXI & !hasHeader) {

    # construct the object from HTSeq files
    dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
                                      directory = dir,
                                      design =  designFormula)
    colnames(dds) <- row.names(sampleTable)

  } else {
      # construct the object using tximport
      library("tximport")
      txiFiles <- as.character(sampleTable$filename)
      labs <- row.names(sampleTable)
      names(txiFiles) <- labs
      if (!is.null(gffFile)) {
        # first need to make the tx2gene table
        # this takes ~2-3 minutes using Bioconductor functions
        suppressPackageStartupMessages({
          library("GenomicFeatures")
        })
        txdb <- makeTxDbFromGFF(gffFile)
        k <- keys(txdb, keytype = "TXNAME")
        tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME")
        # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name)
        tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME)
      }
      try(txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene))
      if (!exists("txi")) {
        # Remove version from transcript IDs in tx2gene...
        tx2gene$TXNAME <- sub('\\.[0-9]+$', '', tx2gene$TXNAME)
        # ...and in txiFiles
        txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene, ignoreTxVersion=TRUE)
      }
      dds <- DESeqDataSetFromTximport(txi,
                                      subset(sampleTable, select=-c(filename)),
                                      designFormula)
  }
  return(dds)
}