Gene Break Detection


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Documentation for package ‘GeneBreak’ version 1.35.0

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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.