bpFilter,CopyNumberBreakPoints-method {GeneBreak} | R Documentation

## bpFilter

### Description

Selects breakpoints by filter criteria options.

### Usage

    ## S4 method for signature 'CopyNumberBreakPoints'
    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

### Details

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

### Value

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

### 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 )

[Package GeneBreak version 1.12.0 Index]