Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 4:5d38abf7e4b6 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 10:43:03 -0500
parents 12fb0d4b1e93
children bde663b872d9
comparison
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3:12fb0d4b1e93 4:5d38abf7e4b6
188 design_matrix <- design_matrix[columns,,drop=FALSE] 188 design_matrix <- design_matrix[columns,,drop=FALSE]
189 189
190 ## Filter for HTSeq predifined counts: 190 ## Filter for HTSeq predifined counts:
191 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique") 191 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique")
192 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned") 192 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned")
193 193 exclude_STAR <- c("N_unmapped", "N_multimapping", "N_noFeature", "N_ambiguous")
194 exclude <- match(c(exclude_HTSeq, exclude_DEXSeq),rownames(read_counts)) 194
195 exclude <- match(c(exclude_HTSeq, exclude_DEXSeq, exclude_STAR),rownames(read_counts))
195 exclude <- exclude[is.na(exclude)==0] 196 exclude <- exclude[is.na(exclude)==0]
196 if(length(exclude) != 0) { 197 if(length(exclude) != 0) {
197 read_counts <- read_counts[-exclude,] 198 read_counts <- read_counts[-exclude,]
198 } 199 }
199 200