Description Slots Accessors Methods Author(s) Examples
An S4 class to represent a CopyNumberBreakPoints object.
A matrix with breakpoints based on segment values
A matrix with breakpoints based on call values
A matrix with segmented copy number values
A matrix with copy number calls
A dataframe with predefined information about the features (usually probes or bins)
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
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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) )
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