jg.runDeSeqR Documentation

jg.runDeSeq

Description

Runs DESeq2 on our peakset after we have obtained the normalised size factors.

Usage

jg.runDeSeq(jg.PeaksetDeSeq, jg.conditions, jg.SizeFactors = NULL)

Arguments

jg.PeaksetDeSeq

is the experimental peakset formatted for DESeq2

jg.conditions

is the list of conditions to be compared

jg.SizeFactors

is the size factors generated from the control samples

Examples

data(jg.controlPeaksetDeSeq,package="Brundle")
data(jg.conditions,package="Brundle")
jg.controlSizeFactors = estimateSizeFactorsForMatrix(jg.controlPeaksetDeSeq)
jg.runDeSeq(jg.controlPeaksetDeSeq,jg.conditions, jg.SizeFactors = NULL)