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
detSigNumPipeline       detSigNumPipeline
determineNumSigs        determineNumSigs
diffCompSigSim          diffCompSigSim
extractCNFeats          extractCNFeats
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
sigSim                  sigSim
sigsExp                 The generated Signatures from the segDataExp
                        run
smoothSegs              smoothSegs
sumOfPosteriors         sumOfPosteriors
validateSegData         validateSegData
