Mercurial > repos > artbio > repenrich
diff edgeR_repenrich.R @ 13:530626b0757c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
author | artbio |
---|---|
date | Tue, 02 Apr 2024 21:16:37 +0000 |
parents | 6bba3e33c2e7 |
children |
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--- a/edgeR_repenrich.R Mon Mar 18 09:39:44 2024 +0000 +++ b/edgeR_repenrich.R Tue Apr 02 21:16:37 2024 +0000 @@ -19,7 +19,6 @@ options(stringAsFactors = FALSE, useFancyQuotes = FALSE) # get options, using the spec as defined by the enclosed list. -# we read the options from the default: commandArgs(TRUE). spec <- matrix( c( "quiet", "q", 0, "logical", @@ -30,8 +29,6 @@ "levelNameB", "B", 1, "character", "levelAfiles", "a", 1, "character", "levelBfiles", "b", 1, "character", - "alignmentA", "i", 1, "character", - "alignmentB", "j", 1, "character", "plots", "p", 1, "character" ), byrow = TRUE, ncol = 4 @@ -65,17 +62,7 @@ counts <- cbind(counts, listB[[element]][, 4]) } colnames(counts) <- c(names(listA[-1]), names(listB[-1])) - -# build aligned counts vector -filesi <- fromJSON(opt$alignmentA, method = "C", unexpected.escape = "error") -filesj <- fromJSON(opt$alignmentB, method = "C", unexpected.escape = "error") -sizes <- c() -for (file in filesi) { - sizes <- c(sizes, read.delim(file, header = TRUE)[1, 1]) -} -for (file in filesj) { - sizes <- c(sizes, read.delim(file, header = TRUE)[1, 1]) -} +sizes <- colSums(counts) # build a meta data object meta <- data.frame( @@ -187,6 +174,3 @@ results$log2FC <- format(results$log2FC, digits = 5) results$FDR <- format(results$FDR, digits = 5) write.table(results, opt$outfile, quote = FALSE, sep = "\t", col.names = TRUE, row.names = FALSE) - -cat("Session information:\n\n") -sessionInfo()