CopyNumberBreakPoints-class {GeneBreak} | R Documentation

## An S4 class to represent a CopyNumberBreakPoints object.

### Description

An S4 class to represent a CopyNumberBreakPoints object.

### Slots

`segmDiff`

  A matrix with breakpoints based on segment values

`callDiff`

  A matrix with breakpoints based on call values

`segments`

  A matrix with segmented copy number values

`calls`

  A matrix with copy number calls

`featureAnnotation`

  A dataframe with predefined information about the features (usually probes or bins)

`featureData`

  A dataframe with calculated information about the features (usually probes or bins)

### 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

### Methods

- getBreakpoints Builds the CopyNumberBreakPoints object from copynumber data and detects breakpoint locations

- bpFilter Selects breakpoints by filter criteria options

- bpStats Applies cohort-based statistics to identify 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 <- bpStats( bp , level = 'feature' , method = 'BH' )
    bpPlot( bp, c(20) )

[Package GeneBreak version 1.16.0 Index]