CopyNumberBreakPointGenes-class {GeneBreak} | R Documentation

## 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

### Author(s)

E. van den Broek and S. van Lieshout

### 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) )

[Package GeneBreak version 1.20.0 Index]