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comparison deseq2.R @ 16:a416957ee305 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b
author iuc
date Fri, 03 Aug 2018 17:23:46 -0400
parents 9a616afdbda5
children d9e5cadc7f0b
comparison
equal deleted inserted replaced
15:9a616afdbda5 16:a416957ee305
201 dir <- "" 201 dir <- ""
202 202
203 if (!useTXI & hasHeader) { 203 if (!useTXI & hasHeader) {
204 countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)}) 204 countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
205 tbl <- do.call("cbind", countfiles) 205 tbl <- do.call("cbind", countfiles)
206 rownames(sampleTable) <- colnames(tbl) # take sample ids from header 206 colnames(tbl) <- rownames(sampleTable) # take sample ids from header
207 207
208 # check for htseq report lines (from DESeqDataSetFromHTSeqCount function) 208 # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
209 oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual", 209 oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual",
210 "not_aligned", "alignment_not_unique") 210 "not_aligned", "alignment_not_unique")
211 specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames 211 specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames