changed the independent filtering method in the DESeq2 results() function from...

changed the independent filtering method in the DESeq2 results() function from the default to independent hypothesis weighting (IHW)

dge_workflow/featcounts_deseq_mf.R

@@ -56,6 +56,7 @@ library(knitr)
 #biocLite("DESeq2")
 library(DESeq2)
 #load_pack(readr)
+library(IHW)
 
 
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/core_commons.R")
@@ -464,8 +465,8 @@ summary(results(dds))
 deResults = plyr::alply(contrasts, 1, plyr::splat(function(condition_1, condition_2){
     #DEBUG condition_1=as_df(contrasts)[1,1]; condition_2=as_df(contrasts)[1,2]
     # results(dds, contrast=c(contrastAttribute, condition_1, condition_2)) %>%
-    # results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff, filterFun = ihw) %>%
-    results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff) %>%
+    results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff, filterFun = ihw) %>%
+    # results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff) %>%
         as_tibble() %>%
         tibble::rownames_to_column("ensembl_gene_id") %>%
     ## see http://rpackages.ianhowson.com/bioc/DESeq2/man/results.html when using contrasts argument