Commit cc1ea6c7 authored by Lena Hersemann's avatar Lena Hersemann

read in sub_data option as logical parameter

parent 1a51ffa3
......@@ -71,7 +71,8 @@ count_matrix_file = opts$count_matrix
design_matrix_file = opts$design_matrix
contrasts_file = opts$contrasts
use_betaPrior = as.logical(opts$betaprior)
sub_data = opts$sub_data
sub_data = as.logical(opts$sub_data)
assert(isTRUE(sub_data), "invalid sub_data boolean")
gene_info_file = opts$gene_info
assert(is.null(gene_info_file) || file.exists(gene_info_file), "invalid gene_info_file")
......@@ -790,7 +791,7 @@ deAnnot %>%
# subset data according to contrasts
if(sub_data == "TRUE"){
if (isTRUE(sub_data)) {
dir.create("de_results")
comp <- apply(contrasts, 1, paste0, collapse = "_vs_")
lapply(comp, function(x) {
......@@ -799,8 +800,7 @@ if(sub_data == "TRUE"){
select(-contrast) %>%
write_tsv(paste("de_results/", x, ".txt", sep =""))
})
} else {}
}
## todo understand purpose and effeect of indpendentFiltering (see https://support.bioconductor.org/p/57128/)
......
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