# HG changeset patch # User artbio # Date 1515403284 18000 # Node ID 6b990f6c6ba91cb2adfe1a72ccdfbe5028b237c9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73 diff -r 000000000000 -r 6b990f6c6ba9 deseq2_normalization.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2_normalization.xml Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,109 @@ + + of hit lists (geometric method) + + bioconductor-deseq2 + + + + + + + + ## 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(DESeq2)) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) + rownames( countsTable )= countsTable[,1] + countsTable= countsTable[ , -1 ] + conds = factor(c(rep ("C", length(countsTable[1,])-1 ), "T")) + cds = DESeqDataSetFromMatrix(countsTable, DataFrame(conds), ~ conds) + cds = estimateSizeFactors( cds ) + write.table (as.data.frame(sizeFactors(cds)), file="${output_factors}", row.names=TRUE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + norm_table = as.data.frame(counts( cds, normalized=TRUE )) + norm_table = cbind(rownames(norm_table), norm_table) + colnames(norm_table) = c("gene", colnames(countsTable) ) + write.table (norm_table, file="${norm_hit_table}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + + + + + + + + + + + + + + + + + + +**What it does** + +DESeq2_normalization takes a tabular table of raw read counts (integers), each column corresponding to a sample count, +and returns (1) the DESeq2 Size Factors (geometic mean method) and (2) a normalized table (floatting number) +of counts. + +**Inputs** + +The following table gives an example of the tabular input that has to be provided to the tool: + + + + + + + 10.1186/s13059-014-0550-8 + + diff -r 000000000000 -r 6b990f6c6ba9 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46 53 +NM_027528 2 0 0 0 0 +NM_011070 1429 1183 1293 1140 902 +NM_013489 0 0 0 0 0 diff -r 000000000000 -r 6b990f6c6ba9 test-data/norm_factors.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm_factors.tab Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,6 @@ +sizeFactors(cds) +2: Oocyte 1: accepted_hits 1.06133711644639 +3: Oocyte 2: accepted_hits 1.10788970615123 +4: Pronuclei 1: accepted_hits 1.1873071040134 +5: pronuclei 2: accepted_hits 0.901037373821142 +6: Pronuclei 3: accepted_hits 0.869190376687854 diff -r 000000000000 -r 6b990f6c6ba9 test-data/norm_table.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm_table.tab Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,500 @@ +gene 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 2951.93671402921 2054.35612169983 1927.04986963017 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