highlightFilters {QDNAseq} | R Documentation |
Highlights data points in a plotted profile to evaluate filtering
Description
Highlights data points in a plotted profile to evaluate filtering.
Usage
highlightFilters(object, col="red", residual=NA, blacklist=NA, mappability=NA, bases=NA,
type="union", ...)
Arguments
object |
A QDNAseqCopyNumbers object.
|
col |
The color used for highlighting.
|
residual |
Either a logical specifying whether to filter based on
loess residuals of the calibration set, or if a numeric , the cutoff
as number of standard deviations estimated with
madDiff to use for. Default is TRUE , which
corresponds to 4.0 standard deviations.
|
blacklist |
Either a logical specifying whether to filter based on
overlap with blacklisted regions, or if numeric, the maximum
percentage of overlap allowed. Default is TRUE , which corresponds to
no overlap allowed (i.e. value of 0).
|
mappability |
A numeric in [0,100] to specify filtering out
bins with mappabilities lower than the number specified. NA (default)
or FALSE will not filter based on mappability.
|
bases |
A numeric specifying the minimum percentage of characterized
bases (not Ns) in the reference genome sequence. NA (default) or
FALSE will not filter based on uncharacterized bases.
|
type |
When specifying multiple filters (residual ,
blacklist , mappability , bases ), whether to
highlight their union (default) or intersection .
|
... |
Further arguments to points .
|
Author(s)
Ilari Scheinin
Examples
data(LGG150)
readCounts <- LGG150
plot(readCounts)
highlightFilters(readCounts, residual=TRUE, blacklist=TRUE)
[Package
QDNAseq version 1.30.0
Index]