Mercurial > repos > iuc > limma_voom

comparison limma_voom.R @ 12:81796eb60bd0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
author iuc
date Sun, 05 Aug 2018 05:13:12 -0400
parents 7e8af58c8052
children d5a940112511
comparison
equal deleted inserted replaced
11:7e8af58c8052 12:81796eb60bd0
164 "contrastData", "C", 1, "character", 164 "contrastData", "C", 1, "character",
165 "cpmReq", "c", 1, "double", 165 "cpmReq", "c", 1, "double",
166 "totReq", "y", 0, "logical", 166 "totReq", "y", 0, "logical",
167 "cntReq", "z", 1, "integer", 167 "cntReq", "z", 1, "integer",
168 "sampleReq", "s", 1, "integer", 168 "sampleReq", "s", 1, "integer",
169 "filtCounts", "F", 0, "logical",
169 "normCounts", "x", 0, "logical", 170 "normCounts", "x", 0, "logical",
170 "rdaOpt", "r", 0, "logical", 171 "rdaOpt", "r", 0, "logical",
171 "lfcReq", "l", 1, "double", 172 "lfcReq", "l", 1, "double",
172 "pValReq", "p", 1, "double", 173 "pValReq", "p", 1, "double",
173 "pAdjOpt", "d", 1, "character", 174 "pAdjOpt", "d", 1, "character",
214 215
215 if (is.null(opt$annoPath)) { 216 if (is.null(opt$annoPath)) {
216 haveAnno <- FALSE 217 haveAnno <- FALSE
217 } else { 218 } else {
218 haveAnno <- TRUE 219 haveAnno <- TRUE
220 }
221
222 if (is.null(opt$filtCounts)) {
223 wantFilt <- FALSE
224 } else {
225 wantFilt <- TRUE
219 } 226 }
220 227
221 if (is.null(opt$normCounts)) { 228 if (is.null(opt$normCounts)) {
222 wantNorm <- FALSE 229 wantNorm <- FALSE
223 } else { 230 } else {
362 stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf")) 369 stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
363 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png")) 370 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
364 topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv")) 371 topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
365 glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html")) 372 glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
366 } 373 }
367 374 filtOut <- makeOut(paste0(deMethod, "_filtcounts.tsv"))
368 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv")) 375 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
369 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData")) 376 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
370 sessionOut <- makeOut("session_info.txt") 377 sessionOut <- makeOut("session_info.txt")
371 378
372 # Initialise data for html links and images, data frame with columns Label and 379 # Initialise data for html links and images, data frame with columns Label and
437 } 444 }
438 } 445 }
439 446
440 data$counts <- data$counts[keep, ] 447 data$counts <- data$counts[keep, ]
441 data$genes <- data$genes[keep, , drop=FALSE] 448 data$genes <- data$genes[keep, , drop=FALSE]
449
450 if (wantFilt) {
451 print("Outputting filtered counts")
452 filt_counts <- data.frame(data$genes, data$counts)
453 write.table(filt_counts, file=filtOut, row.names=FALSE, sep="\t", quote=FALSE)
454 linkData <- rbind(linkData, data.frame(Label=paste0(deMethod, "_", "filtcounts.tsv"), Link=paste0(deMethod, "_", "filtcounts.tsv"), stringsAsFactors=FALSE))
455 }
442 456
443 # Plot Density 457 # Plot Density
444 if ("d" %in% plots) { 458 if ("d" %in% plots) {
445 # PNG 459 # PNG
446 png(denOutPng, width=1000, height=500) 460 png(denOutPng, width=1000, height=500)