R: Call mutation burden

callMutationBurden {PureCN}

R Documentation

Call mutation burden

Description

This function provides detailed mutation burden information.

Usage

callMutationBurden(res, id = 1, remove.flagged = TRUE,
  min.prior.somatic = 0.1, max.prior.somatic = 1, min.cellfraction = 0,
  fun.countMutation = function(vcf) width(vcf) == 1, callable = NULL,
  exclude = NULL)

Arguments

`res`	Return object of the `runAbsoluteCN` function.
`id`	Candidate solution to extract mutation burden from. `id=1` will use the maximum likelihood solution.
`remove.flagged`	Remove variants flagged by `predictSomatic`.
`min.prior.somatic`	Exclude variants with somatic prior probability lower than this cutoff.
`max.prior.somatic`	Exclude variants with somatic prior probability higher than this cutoff. This is useful for removing hotspot mutations in small panels that might inflate the mutation burden.
`min.cellfraction`	Exclude variants with cellular fraction lower than this cutoff. These are sub-clonal mutations or artifacts with very low allelic fraction.
`fun.countMutation`	Function that can be used to filter the input VCF further for filtering, for example to only keep missense mutations. Expects a `logical` vector indicating whether variant should be counted (`TRUE`) or not (`FALSE`). Default is to keep only single nucleotide variants.
`callable`	`GRanges` object with callable genomic regions, for example obtained by ‘GATK CallableLoci’ BED file, imported with `rtracklayer`.
`exclude`	`GRanges` object with genomic regions that should be excluded from the `callable` regions, for example intronic regions. Requires `callable`.

Value

Returns data.frame with mutation counts and sizes of callable regions.

Author(s)

Markus Riester

Examples


data(purecn.example.output)
callMutationBurden(purecn.example.output)

# To calculate exact mutations per megabase, we can provide a BED
# file containing all callable regions
callableBed <- import(system.file("extdata", "example_callable.bed.gz", 
    package = "PureCN"))

# We can exclude some regions for mutation burden calculation, 
# for example intronic regions. 
exclude <- GRanges(seqnames="chr1", IRanges(start=1, 
    end=max(end(callableBed))))

# We can also exclude specific mutations by filtering the input VCF
myVcfFilter <- function(vcf) seqnames(vcf)!="chr2"

callsCallable <- callMutationBurden(purecn.example.output, 
    callable=callableBed, exclude=exclude, fun.countMutation=myVcfFilter)

[Package PureCN version 1.10.0 Index]