From cf9fc936800f211661cace1f2c38c742b504f527 Mon Sep 17 00:00:00 2001
From: Naharajan <dilln2002@gmail.com>
Date: Tue, 8 Mar 2016 11:14:02 +0100
Subject: [PATCH] Problem with plotDispEsts resolved by callign DESeq before
and also loaded readr library for write_tsv
---
dge_workflow/featcounts_deseq.R | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/dge_workflow/featcounts_deseq.R b/dge_workflow/featcounts_deseq.R
index 4926141..fea78b5 100755
--- a/dge_workflow/featcounts_deseq.R
+++ b/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)
--
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