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

Description Slots Accessors Methods Author(s) Examples

An S4 class to represent a CopyNumberBreakPoints object.

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)

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

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

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 <- bpStats( bp , level = 'feature' , method = 'BH' )
bpPlot( bp, c(20) )