comparison deseq2.R @ 16:a416957ee305 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b

15:9a616afdbda5

dir <- ""

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

16:a416957ee305

dir <- ""

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