# HG changeset patch # User mvdbeek # Date 1457179372 18000 # Node ID da2dbe13adc2386a5bf966abea11ebaf84228b06 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty diff -r 000000000000 -r da2dbe13adc2 replicateDESeq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/replicateDESeq.xml Sat Mar 05 07:02:52 2016 -0500 @@ -0,0 +1,49 @@ + + with sample replicates + + R + biocbasics + + Rscript $replicateDESeq + + + + + + + + + + + + + + + + + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + suppressMessages(require(DESeq)) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) + rownames( countsTable )= countsTable[,1] + countsTable= countsTable[ , -1 ] + stringconds = "${expPlan}" + conds = unlist(strsplit(stringconds, split="")) + cds = newCountDataSet( countsTable, conds ) + cds = estimateSizeFactors( cds ) + cds = estimateDispersions( cds, method="per-condition", sharingMode="maximum") ## was fit-only before 9-12-2013 !! tried for RNAseq - Actually does not change anything ! + ## Attention: fitType="local" is added when parametricDispersionFit fails. remove after use ! + res = nbinomTest( cds, "C", "T" ) + # resNA = res[-which(is.na(res[,8])),] ## omitted the NA lignes, but this was causing a full delete of the table completely devoid of NA !! (not logical but true) + write.table ( res[order(res[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + + + + +**What it does** + +DESeq differential calling (order by padj, ascending), on more than two samples, with replicates. + + + + diff -r 000000000000 -r da2dbe13adc2 test-data/counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Sat Mar 05 07:02:52 2016 -0500 @@ -0,0 +1,500 @@ +Geneid 2: Oocyte 1: accepted_hits 3: Oocyte 2: accepted_hits 4: Pronuclei 1: accepted_hits 5: pronuclei 2: accepted_hits 6: Pronuclei 3: accepted_hits +NM_001195025 0 0 0 0 0 +NM_028778 0 0 0 0 0 +NM_001290393 0 0 0 0 0 +NM_008922 3133 2276 2288 2659 820 +NM_175370 4 22 7 16 9 +NM_001290390 0 0 0 0 0 +NM_175642 977 1711 1013 459 430 +NM_001290392 0 0 0 0 0 +NM_027671 0 0 0 0 0 +NM_178884 0 0 0 2 3 +NM_199021 332 413 1436 836 1018 +NM_198680 0 0 0 0 0 +NM_011465 0 4 0 0 0 +NM_130890 0 0 0 0 0 +NM_001113393 0 0 0 0 0 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.*? .*? .*? .*? .*? .*? +NM\_013489\ .*? .*? .*? .*? .*? .*? .*? diff -r 000000000000 -r da2dbe13adc2 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Mar 05 07:02:52 2016 -0500 @@ -0,0 +1,9 @@ + + + + + + + + +