run_deseq2: Run DESeq2 analysis

In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R

Description

Function to run DESeq2 analysis on a DDS object and to extract the desired contrasts.

Usage

run_deseq2(dds = dds, p.value = 0.05, adjust.method = "BH")

Arguments

dds	DESeq2 dds object created by DESeqDataSetFromMatrix.
p.value	p-value for determining signficance for differential expression.
adjust.method	method for p-value correction for multiple testing

Value

A DDS object in which has undergone dispersion estimates and model fitting.

Examples

## Not run: 
dds <- run_deseq2(dds = ddsMat)

## End(Not run)

anilchalisey/parseR documentation built on May 7, 2019, 7:45 a.m.