accessOptions,CopyNumberBreakPoints-method
                        Access Object Data. This method lists possible
                        functions to access the data of the object.
addGeneAnnotation,CopyNumberBreakPoints-method
                        addGeneAnnotation
bpFilter,CopyNumberBreakPoints-method
                        bpFilter
bpGenes,CopyNumberBreakPointGenes-method
                        bpGenes
bpPlot,CopyNumberBreakPoints-method
                        bpPlot
bpStats,CopyNumberBreakPoints-method
                        bpStats
breakpointData,CopyNumberBreakPoints-method
                        Access Object breakpointData. This method
                        returns a dataframe with breakpoint values per
                        feature.
breakpointsPerGene,CopyNumberBreakPointGenes-method
                        Access Object breakpointsPerGene. This method
                        returns a dataframe with breakpoints per gene.
callData,CopyNumberBreakPoints-method
                        Access Object callData. This method returns a
                        dataframe with feature call values.
copynumber.data.chr18   CGHcall Example copynumber data hg18 chr18
copynumber.data.chr20   CGHcall Example copynumber data hg18 chr20
copynumber.data.chr21   CGHcall Example copynumber data hg18 chr21
CopyNumberBreakPointGenes-class
                        An S4 class to represent a
                        CopyNumberBreakPointGenes object
CopyNumberBreakPoints-class
                        An S4 class to represent a
                        CopyNumberBreakPoints object.
ens.gene.ann.hg18       Gene Annotation hg18
ens.gene.ann.hg19       Gene Annotation hg19
ens.gene.ann.hg38       Gene Annotation hg38
featureChromosomes,CopyNumberBreakPoints-method
                        Access Object featureChromosomes. This method
                        returns a vector with feature chromosomes.
featureInfo,CopyNumberBreakPoints-method
                        Access Options featureInfo. This method returns
                        a dataframe with feature annotations.
featuresPerGene,CopyNumberBreakPointGenes-method
                        Access Object featuresPerGene. This method
                        returns a vector with gene-related features for
                        a particular gene.
GeneBreak               GeneBreak: A package for gene breakpoint
                        detection on copy number abberation data
geneChromosomes,CopyNumberBreakPointGenes-method
                        Access Object geneChromosomes. This method
                        returns a vector with gene chromosomes.
geneInfo,CopyNumberBreakPointGenes-method
                        Access Options geneInfo. This method returns a
                        dataframe with gene annotations.
getBreakpoints          getBreakpoints
namesFeatures,CopyNumberBreakPoints-method
                        Access Object namesFeatures. This method
                        returns a vector with feature names.
recurrentGenes,CopyNumberBreakPointGenes-method
                        Access Options recurrentGenes. This method
                        returns a dataframe that contains genes that
                        are recurrently affected across samples based
                        on a FDR threshold.
sampleNames,CopyNumberBreakPoints-method
                        Access Object sampleNames. This method returns
                        a vector with sample names.
segmentData,CopyNumberBreakPoints-method
                        Access Object segmentData. This method returns
                        a dataframe with segment values.
