# Gene Break Detection

## Documentation for package ‘GeneBreak’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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