fixed output prefixing in limma workflow

dge_workflow/limma/dge_limma.R

@@ -48,7 +48,7 @@ designFormula = opts$design
 assert(str_detect(designFormula, ".*condition$"))
 
 
-results_prefix = if (str_length(opts$out) > 0) paste0(opts$out, ".") else "" # used by add_prefix
+results_prefix = if (str_length(opts$out) > 0) opts$out else "" # used by add_prefix
 
 pcutoff = if (is.null(opts$pcutoff))NULL else as.numeric(opts$pcutoff)
 qcutoff = if (is.numeric(pcutoff))NULL else as.numeric(opts$qcutoff)
@@ -68,14 +68,22 @@ vec_as_df(unlist(opts)) %>%
 #' The working directory of the analysis was: `r getwd()`
 
 ## both batches combines
-
-contrasts = read_tsv(contrasts_file) %T>% { print(kable(.))}
 expDesign = read_tsv(design_matrix_file) %T>% glimpse
 # countData = read_tsv(interp_from_env("../logms_inten_matrix_acc.txt")) %T>% glimpse
 countData = read_tsv(count_matrix_file) %T>% glimpse
 
 names(countData)[1] = "gene_id"
 
+if (! is.null(contrasts_file)) {
+    contrasts = read_tsv(contrasts_file) %T>% { print(kable(.))}
+}else {
+    contrasts = select(expDesign, condition) %>% distinct %>%
+        merge(., ., suffixes = c("_1", "_2"), by = NULL) %>%
+        filter(ac(condition_1) > ac(condition_2))
+    # write_tsv(contrasts, paste(resultsBase, "contrasts.txt"))
+}
+
+
 
 # zero-imputation is disabled here because this should be better implement per experiment
 # countData %<>% mutate_if(is.numeric, funs(replace(., is.na(.), 0)))