jg.runDeSeq: jg.runDeSeq

Description Usage Arguments Examples

Description

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

Usage

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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

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

Brundle documentation built on May 2, 2019, 10:14 a.m.