GeneBreak (version 1.2.0)

CopyNumberBreakPointGenes-class: An S4 class to represent a CopyNumberBreakPointGenes object

Description

An S4 class to represent a CopyNumberBreakPointGenes object

Slots

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

Accessors

• 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

Methods

• 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

Examples

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) )