comparison edger.R @ 5:fb9b9f0f2f06 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476

4:4730985c816f

    countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)})
    counts <- do.call("cbind", countfiles)
    
} else {
    # Process the single count matrix
    counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE)
    row.names(counts) <- counts[, 1]
    counts <- counts[ , -1]
    countsRows <- nrow(counts)

    # Process factors
    if (is.null(opt$factInput)) {
            factorData <- read.table(opt$factFile, header=TRUE, sep="\t", strip.white=TRUE)
            # order samples as in counts matrix
            factorData <- factorData[match(colnames(counts), factorData[, 1]), ]
            factors <- factorData[, -1, drop=FALSE]
    }  else {
            factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))

    }
}

 # if annotation file provided
if (haveAnno) {
    geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", stringsAsFactors=FALSE)
}

#Create output directory
dir.create(opt$outPath, showWarnings=FALSE)

5:fb9b9f0f2f06

    countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)})
    counts <- do.call("cbind", countfiles)
    
} else {
    # Process the single count matrix
    counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", strip.white=TRUE, stringsAsFactors=FALSE)
    row.names(counts) <- counts[, 1]
    counts <- counts[ , -1]
    countsRows <- nrow(counts)

    # Process factors
    if (is.null(opt$factInput)) {
            factorData <- read.table(opt$factFile, header=TRUE, sep="\t", strip.white=TRUE)
            # check samples names match
            if(!any(factorData[, 1] %in% colnames(counts)))
                stop("Sample IDs in factors file and count matrix don't match")
            # order samples as in counts matrix
            factorData <- factorData[match(colnames(counts), factorData[, 1]), ]
            factors <- factorData[, -1, drop=FALSE]
    }  else {
            factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))

    }
}

 # if annotation file provided
if (haveAnno) {
    geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE)
}

#Create output directory
dir.create(opt$outPath, showWarnings=FALSE)