CopyNumberBreakPointGenes-class: An S4 class to represent a CopyNumberBreakPointGenes object
In GeneBreak: Gene Break Detection

Description Slots Accessors Methods Author(s) Examples

An S4 class to represent a CopyNumberBreakPointGenes object

geneAnnotation: A data.frame with original gene annotation input
geneData: A data.frame with gene information added by package methods
featuresPerGene: A list with the associated features per gene
breakpointsPerGene: A matrix with breakage status per gene

callData( object ) Returns feature call values:
segmentData( object ) Returns feature segment values
breakpointData( object ) Returns feature breakpoint values
sampleNames( object ) Returns vector with sample names
namesFeatures( object ) Returns vector with feature names
featureChromosomes( object ) Returns vector of feature chromosomes
featureInfo( object ) Returns feature data/information
geneChromosomes( object ) Returns vector of gene chromosomes
geneInfo( object ) Returns gene data/information
featuresPerGene( object ) Returns a list of genes with coupled features
breakpointsPerGene( object ) Returns gene break status
recurrentGenes( object ) Returns recurrently broken genes

getBreakpoints Builds the CopyNumberBreakPoints object from copynumber data and detects breakpoint locations
bpFilter Selects breakpoints by filter criteria options
addGeneAnnotation Maps features to gene locations
bpGenes Indentifies genes affected by breakpoint locations
bpStats Applies cohort-based statistics to identify genes and/or chromosomal locations that are recurrently affected by breakpoints
bpPlot Plots breakpoint frequencies per chromosome

E. van den Broek and S. van Lieshout

data( copynumber.data.chr20 )
data( ens.gene.ann.hg18 )
bp <- getBreakpoints( copynumber.data.chr20 )
bp <- bpFilter( bp )
bp <- addGeneAnnotation( bp, ens.gene.ann.hg18 )
bp <- bpGenes( bp )
bp <- bpStats( bp )
bpPlot( bp, c(20) )