GeneBreak (version 1.2.0)

bpFilter,CopyNumberBreakPoints-method: bpFilter

Description

Selects breakpoints by filter criteria options.

Usage

"bpFilter"(object, filter = "CNA-ass", threshold = NULL)

Arguments

object

An object of class CopyNumberBreakPoints

filter

Type of filter. This can be either "CNA-ass", "deltaSeg" or "deltaCall".

• CNA-ass: filter out breakpoints that are flanked by copy number neutral segments to obtain CNA-associated breakpoint locations
• deltaSeg: selects for breakpoints where the log2 ratio transition of the copy number segments exceeds the user-defined threshold
• deltaCall: selects only breakpoints of discrete copy number states (amplification, gain, neutral, loss)

threshold

Set the minimal log2 ratio difference between segments. This parameter is required for the "deltaSeg" filter option

Value

Returns an object of class CopyNumberBreakPoints with breakpoint matrix replaced by filtered breakpoints.

Details

Filter options "CNA-ass" and "deltaCall" require calls in addition to segmented copynumber data (see input for getBreakpoints() )

Examples

data( copynumber.data.chr20 )
bp <- getBreakpoints( copynumber.data.chr20 )
bp <- bpFilter( bp, filter = "CNA-ass" )
bp <- bpFilter( bp, filter = "deltaSeg", threshold = 0.2 )

## options to inspect the data
bp
accessOptions( bp )