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comparison edger.R @ 4:4730985c816f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
author iuc
date Sat, 05 Jan 2019 05:32:33 -0500
parents d79ed3ec25fe
children fb9b9f0f2f06
comparison
equal deleted inserted replaced
3:d79ed3ec25fe 4:4730985c816f
266 counts <- counts[ , -1] 266 counts <- counts[ , -1]
267 countsRows <- nrow(counts) 267 countsRows <- nrow(counts)
268 268
269 # Process factors 269 # Process factors
270 if (is.null(opt$factInput)) { 270 if (is.null(opt$factInput)) {
271 factorData <- read.table(opt$factFile, header=TRUE, sep="\t") 271 factorData <- read.table(opt$factFile, header=TRUE, sep="\t", strip.white=TRUE)
272 # order samples as in counts matrix
273 factorData <- factorData[match(colnames(counts), factorData[, 1]), ]
272 factors <- factorData[, -1, drop=FALSE] 274 factors <- factorData[, -1, drop=FALSE]
273 } else { 275 } else {
274 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE)) 276 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))
275 factorData <- list() 277 factorData <- list()
276 for (fact in factors) { 278 for (fact in factors) {