jg.runDeSeq: jg.runDeSeq
In Brundle: Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data

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

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

`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

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