applyFilters {QDNAseq} | R Documentation |
Adjusts the filtering on which bins are used
Description
Adjusts the filtering on which bins are used.
Usage
applyFilters(object, residual=TRUE, blacklist=TRUE, mappability=NA, bases=NA,
chromosomes=c("X", "Y"))
Arguments
object |
A QDNAseqReadCounts object.
|
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 allowd (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 filted based on uncharacterized bases.
|
chromosomes |
A character vector specifying which chromosomes
to filter out. Defaults to the sex chromosomes and mitochondria,
i.e. c("X", "Y", "MT") .
|
Value
Returns a QDNAseqReadCounts
object with updated filtering.
Author(s)
Ilari Scheinin
Examples
data(LGG150)
readCounts <- LGG150
readCountsFiltered <- applyFilters(readCounts)
[Package
QDNAseq version 1.18.0
Index]