Gene Break Detection

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Documentation for package ‘GeneBreak’ version 1.35.0

• 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.