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"), 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)

[Package QDNAseq version 1.24.0 Index]