Commit ccd20785 authored by Holger Brandl's avatar Holger Brandl

Merge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_tools

parents 9839905f cc1ea6c7
...@@ -71,7 +71,8 @@ count_matrix_file = opts$count_matrix ...@@ -71,7 +71,8 @@ count_matrix_file = opts$count_matrix
design_matrix_file = opts$design_matrix design_matrix_file = opts$design_matrix
contrasts_file = opts$contrasts contrasts_file = opts$contrasts
use_betaPrior = as.logical(opts$betaprior) use_betaPrior = as.logical(opts$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$gene_info gene_info_file = opts$gene_info
assert(is.null(gene_info_file) || file.exists(gene_info_file), "invalid gene_info_file") assert(is.null(gene_info_file) || file.exists(gene_info_file), "invalid gene_info_file")
...@@ -790,7 +791,7 @@ deAnnot %>% ...@@ -790,7 +791,7 @@ deAnnot %>%
# subset data according to contrasts # subset data according to contrasts
if(sub_data == "TRUE"){ if (isTRUE(sub_data)) {
dir.create("de_results") dir.create("de_results")
comp <- apply(contrasts, 1, paste0, collapse = "_vs_") comp <- apply(contrasts, 1, paste0, collapse = "_vs_")
lapply(comp, function(x) { lapply(comp, function(x) {
...@@ -799,8 +800,7 @@ if(sub_data == "TRUE"){ ...@@ -799,8 +800,7 @@ if(sub_data == "TRUE"){
select(-contrast) %>% select(-contrast) %>%
write_tsv(paste("de_results/", x, ".txt", sep ="")) write_tsv(paste("de_results/", x, ".txt", sep =""))
}) })
} else {} }
## todo understand purpose and effeect of indpendentFiltering (see https://support.bioconductor.org/p/57128/) ## todo understand purpose and effeect of indpendentFiltering (see https://support.bioconductor.org/p/57128/)
......
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