Problem with plotDispEsts resolved by callign DESeq before and also loaded...

Problem with plotDispEsts resolved by callign DESeq before and also loaded readr library for write_tsv

dge_workflow/featcounts_deseq.R

@@ -24,6 +24,7 @@ opts <- docopt(doc, commandArgs(TRUE))
 
 require(knitr)
 require(DESeq2)
+library(readr)
 
 
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/core_commons.R")
@@ -128,7 +129,7 @@ if(!all((contrasts %>% gather %$% value %>% unique) %in% colData$condition)){
 dds <- DESeqDataSetFromMatrix(countMatrix, colData, formula(~ condition))
 #dds <- estimateSizeFactors(dds)
 #dds <- estimateDispersions(dds)
-
+dds <- DESeq(dds)
 
 ########################################################################################################################
 #' ## Quality Control
@@ -199,7 +200,7 @@ sizeFactors(dds) %>%
 #' Run Deseq Test
 #dds <- DESeq(dds, fitType='local', betaPrior=FALSE)
 #dds <- DESeq(dds, fitType='local')
-dds <- DESeq(dds)
+#dds <- DESeq(dds)
 
 #res <- results(dds)
 #resultsNames(dds)