bpFilter,CopyNumberBreakPoints-method {GeneBreak} | R Documentation |
Selects breakpoints by filter criteria options.
## S4 method for signature 'CopyNumberBreakPoints' bpFilter(object, filter = "CNA-ass", threshold = NULL)
object |
An object of class CopyNumberBreakPoints |
filter |
Type of filter. This can be either "CNA-ass", "deltaSeg" or "deltaCall".
|
threshold |
Set the minimal log2 ratio difference between segments. This parameter is required for the "deltaSeg" filter option |
Filter options "CNA-ass" and "deltaCall" require calls in addition to segmented copynumber data (see input for getBreakpoints()
)
Returns an object of class CopyNumberBreakPoints with breakpoint matrix replaced by filtered breakpoints.
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 )