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comparison edger.R @ 5:fb9b9f0f2f06 draft

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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
comparison
equal deleted inserted replaced
4:4730985c816f 5:fb9b9f0f2f06
259 countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)}) 259 countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)})
260 counts <- do.call("cbind", countfiles) 260 counts <- do.call("cbind", countfiles)
261 261
262 } else { 262 } else {
263 # Process the single count matrix 263 # Process the single count matrix
264 counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE) 264 counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", strip.white=TRUE, stringsAsFactors=FALSE)
265 row.names(counts) <- counts[, 1] 265 row.names(counts) <- counts[, 1]
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$factFile, header=TRUE, sep="\t", strip.white=TRUE) 271 factorData <- read.table(opt$factFile, header=TRUE, sep="\t", strip.white=TRUE)
272 # check samples names match
273 if(!any(factorData[, 1] %in% colnames(counts)))
274 stop("Sample IDs in factors file and count matrix don't match")
272 # order samples as in counts matrix 275 # order samples as in counts matrix
273 factorData <- factorData[match(colnames(counts), factorData[, 1]), ] 276 factorData <- factorData[match(colnames(counts), factorData[, 1]), ]
274 factors <- factorData[, -1, drop=FALSE] 277 factors <- factorData[, -1, drop=FALSE]
275 } else { 278 } else {
276 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE)) 279 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))
291 } 294 }
292 } 295 }
293 296
294 # if annotation file provided 297 # if annotation file provided
295 if (haveAnno) { 298 if (haveAnno) {
296 geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", stringsAsFactors=FALSE) 299 geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE)
297 } 300 }
298 301
299 #Create output directory 302 #Create output directory
300 dir.create(opt$outPath, showWarnings=FALSE) 303 dir.create(opt$outPath, showWarnings=FALSE)
301 304