Mercurial > repos > iuc > limma_voom
diff limma_voom.R @ 12:81796eb60bd0 draft
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 |
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--- a/limma_voom.R Mon Jun 11 08:18:25 2018 -0400 +++ b/limma_voom.R Sun Aug 05 05:13:12 2018 -0400 @@ -166,6 +166,7 @@ "totReq", "y", 0, "logical", "cntReq", "z", 1, "integer", "sampleReq", "s", 1, "integer", + "filtCounts", "F", 0, "logical", "normCounts", "x", 0, "logical", "rdaOpt", "r", 0, "logical", "lfcReq", "l", 1, "double", @@ -218,6 +219,12 @@ haveAnno <- TRUE } +if (is.null(opt$filtCounts)) { + wantFilt <- FALSE +} else { + wantFilt <- TRUE +} + if (is.null(opt$normCounts)) { wantNorm <- FALSE } else { @@ -364,7 +371,7 @@ topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv")) glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html")) } - +filtOut <- makeOut(paste0(deMethod, "_filtcounts.tsv")) normOut <- makeOut(paste0(deMethod, "_normcounts.tsv")) rdaOut <- makeOut(paste0(deMethod, "_analysis.RData")) sessionOut <- makeOut("session_info.txt") @@ -440,6 +447,13 @@ data$counts <- data$counts[keep, ] data$genes <- data$genes[keep, , drop=FALSE] + if (wantFilt) { + print("Outputting filtered counts") + filt_counts <- data.frame(data$genes, data$counts) + write.table(filt_counts, file=filtOut, row.names=FALSE, sep="\t", quote=FALSE) + linkData <- rbind(linkData, data.frame(Label=paste0(deMethod, "_", "filtcounts.tsv"), Link=paste0(deMethod, "_", "filtcounts.tsv"), stringsAsFactors=FALSE)) + } + # Plot Density if ("d" %in% plots) { # PNG