R: Analysis of Copy Number Signatures

# Analysis of Copy Number Signatures

## Documentation for package ‘CNSigs’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

addPloidyData | addPloidyData
cancerComps | Components derived from TCGA
cancerSigs | Signatures derived from TCGA
checkCompOverlap | checkCompOverlap
collapsedSigs | Signatures derived from TCGA and collapsed.
compareExposures | compareExposures
compsExp | Components fitted onto featsExp
createSigs | createSigs
defaultFeats | Default features to use for copy number signatures
determineNumSigs | determineNumSigs
detSigNumPipeline | detSigNumPipeline
diffCompSigSim | diffCompSigSim
extractBP10MB | featureFuncs
extractBPChrArm | featureFuncs
extractChangepoints | featureFuncs
extractCN | featureFuncs
extractCNFeats | extractCNFeats
extractOscillations | featureFuncs
extractSegsize | featureFuncs
featsExp | Features from segDataExp
findExposures | findExposures
fitComponent | fitComponent
fitModels | fitModels
generateSCM | generateSCM
matchSigs | matchSigs
plotComp | plotComp
plotComps | plotComps
plotScm | plotScm
plotSegs | plotSegs
plotSig | plotSig
plotSigExposure | plotSigExposure
plotSigExposureMat | plotSigExposureMat
plotSigMat | plotSigMat
plotSigs | plotSigs
postProb | postProb
readSegs | readSegs
reducePeaks | reducePeaks
referenceExp | The result object from Pipeline using segDataExp.
remapResults | remapResults
runPipeline | runPipeline
scmExp | Sample by component matrix for segDataExp
segDataExp | Segmentation Data from TCGA BRCA samples
segStats | segStats
sigExposExp | The generated sigExposure from the segDataExp run
sigsExp | The generated Signatures from the segDataExp run
sigSim | sigSim
smoothSegs | smoothSegs
sumOfPosteriors | sumOfPosteriors
validateSegData | validateSegData