highlightFilters: 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 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.

type

When specifying multiple filters (residual, blacklist, mappability, bases), whether to highlight their union (default) or intersection.

...

Further arguments to points.

Examples

Run this code

data(LGG150)
readCounts <- LGG150
plot(readCounts)
highlightFilters(readCounts, residual=TRUE, blacklist=TRUE)

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