applyFilters: Adjusts the filtering on which bins are used
In QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

Adjusts the filtering on which bins are used.

1 2	applyFilters(object, residual=TRUE, blacklist=TRUE, mappability=NA, bases=NA, chromosomes=c("X", "Y"), verbose=getOption("QDNAseq::verbose", TRUE))

`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.

Returns a QDNAseqReadCounts object with updated filtering.

Ilari Scheinin

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

QDNAseq documentation built on Nov. 8, 2020, 6:57 p.m.

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