applyFilters: Adjusts the filtering on which bins are used

In ccagc/QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

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"), verbose=getOption("QDNAseq::verbose", TRUE))

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 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.
chromosomes	A character vector specifying which chromosomes to filter out. Defaults to the sex chromosomes and mitochondria, i.e. c("X", "Y", "MT").
verbose	If TRUE, verbose messages are produced.

Value

Returns a QDNAseqReadCounts object with updated filtering.

Author(s)

Ilari Scheinin

Examples

data(LGG150)
readCounts <- LGG150
readCountsFiltered <- applyFilters(readCounts)

ccagc/QDNAseq documentation built on Feb. 2, 2023, 12:56 p.m.