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Last data update: 2014.03.03

R: Adjusts the filtering on which bins are used

applyFilters

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"))

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 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.
`chromosomes`	A `character` vector specifying which chromosomes to filter out. Defaults to the sex chromosomes and mitochondria, i.e. `c("X", "Y", "MT")`.

Value

Returns a QDNAseqReadCounts object with updated filtering.

Author(s)

Ilari Scheinin

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(QDNAseq)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/QDNAseq/applyFilters.Rd_%03d_medium.png", width=480, height=480)
> ### Name: applyFilters
> ### Title: Adjusts the filtering on which bins are used
> ### Aliases: applyFilters applyFilters,QDNAseqReadCounts-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(LGG150)
> readCounts <- LGG150
> readCountsFiltered <- applyFilters(readCounts)
38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>