Mercurial > repos > yhoogstrate > edger_with_design_matrix

diff edgeR_Differential_Gene_Expression.xml @ 118:7e98e8bcfbf7 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387
author yhoogstrate
date Wed, 09 Dec 2015 10:42:33 -0500
parents 6df940f979c8
children 0a05f6a91d71
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--- a/edgeR_Differential_Gene_Expression.xml	Thu Sep 03 09:41:44 2015 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Wed Dec 09 10:42:33 2015 -0500
@@ -190,8 +190,9 @@
 ## Filter for HTSeq predifined counts:
 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique")
 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned")
+exclude_STAR <- c("N_unmapped", "N_multimapping", "N_noFeature", "N_ambiguous")
 
-exclude <- match(c(exclude_HTSeq, exclude_DEXSeq),rownames(read_counts))
+exclude <- match(c(exclude_HTSeq, exclude_DEXSeq, exclude_STAR),rownames(read_counts))
 exclude <- exclude[is.na(exclude)==0]
 if(length(exclude) != 0)  {
   read_counts <- read_counts[-exclude,]