Mercurial > repos > iuc > edger
diff edger.R @ 5:fb9b9f0f2f06 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476
| author | iuc |
|---|---|
| date | Tue, 05 Feb 2019 20:57:30 -0500 |
| parents | 4730985c816f |
| children | 555659de7321 |
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--- a/edger.R Sat Jan 05 05:32:33 2019 -0500 +++ b/edger.R Tue Feb 05 20:57:30 2019 -0500 @@ -261,7 +261,7 @@ } else { # Process the single count matrix - counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE) + counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", strip.white=TRUE, stringsAsFactors=FALSE) row.names(counts) <- counts[, 1] counts <- counts[ , -1] countsRows <- nrow(counts) @@ -269,6 +269,9 @@ # 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] @@ -293,7 +296,7 @@ # if annotation file provided if (haveAnno) { - geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", stringsAsFactors=FALSE) + geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE) } #Create output directory