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) )