CopyNumberBreakPointGenes-class
                        An S4 class to represent a
                        CopyNumberBreakPointGenes object
CopyNumberBreakPoints-class
                        An S4 class to represent a
                        CopyNumberBreakPoints object.
GeneBreak               GeneBreak: A package for gene breakpoint
                        detection on copy number abberation data
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
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.
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.
