jg.runDeSeq: jg.runDeSeq
In andrewholding/Brundle: Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data
Description
Usage
Arguments
Examples
Description
Runs DESeq2 on our peakset after we have obtained the normalised size factors.
Usage
1
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
1
2
3
4
data(jg.controlPeaksetDeSeq,package="Brundle")
data(jg.conditions,package="Brundle")
jg.controlSizeFactors = estimateSizeFactorsForMatrix(jg.controlPeaksetDeSeq)
jg.runDeSeq(jg.controlPeaksetDeSeq,jg.conditions, jg.SizeFactors = NULL)
andrewholding/Brundle documentation built on May 10, 2019, 5:17 a.m.
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Description Usage Arguments Examples
Description
Runs DESeq2 on our peakset after we have obtained the normalised size factors.
Usage
1 | 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
1 2 3 4 | data(jg.controlPeaksetDeSeq,package="Brundle")
data(jg.conditions,package="Brundle")
jg.controlSizeFactors = estimateSizeFactorsForMatrix(jg.controlPeaksetDeSeq)
jg.runDeSeq(jg.controlPeaksetDeSeq,jg.conditions, jg.SizeFactors = NULL)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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