callMutationBurden: Call mutation burden

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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

See Also

runAbsoluteCN predictSomatic

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)

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.