comparison edgeR_Differential_Gene_Expression.xml @ 118:7e98e8bcfbf7 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387

117:6df940f979c8

design_matrix <- design_matrix[columns,,drop=FALSE]

## 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 <- match(c(exclude_HTSeq, exclude_DEXSeq),rownames(read_counts))
exclude <- exclude[is.na(exclude)==0]
if(length(exclude) != 0)  {
  read_counts <- read_counts[-exclude,]
}

118:7e98e8bcfbf7

design_matrix <- design_matrix[columns,,drop=FALSE]

## 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, exclude_STAR),rownames(read_counts))
exclude <- exclude[is.na(exclude)==0]
if(length(exclude) != 0)  {
  read_counts <- read_counts[-exclude,]
}