R: Highlights data points in a plotted profile to evaluate...

highlightFilters {QDNAseq}

R Documentation

Highlights data points in a plotted profile to evaluate filtering

Highlights data points in a plotted profile to evaluate filtering.

highlightFilters(object, col="red", residual=NA, blacklist=NA, mappability=NA, bases=NA,
  type="union", ...)

`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`.

Ilari Scheinin

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

[Package QDNAseq version 1.30.0 Index]