comparison egsea.R @ 2:ba2111ae6eb4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5

1:73281fbdf6c1

    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(args$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE)
    row.names(counts) <- counts[, 1]
    counts <- counts[ , -1]
    countsRows <- nrow(counts)

    # Process factors
    if (is.null(args$factInput)) {
            factorData <- read.table(args$factFile, header=TRUE, sep="\t")
            factors <- factorData[, -1, drop=FALSE]
    }  else {
            factors <- unlist(strsplit(args$factInput, "|", fixed=TRUE))
            factorData <- list()
            for (fact in factors) {

2:ba2111ae6eb4

    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(args$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE, check.names=FALSE)
    row.names(counts) <- counts[, 1]
    counts <- counts[ , -1]
    countsRows <- nrow(counts)

    # Process factors
    if (is.null(args$factInput)) {
            factorData <- read.table(args$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(args$factInput, "|", fixed=TRUE))
            factorData <- list()
            for (fact in factors) {