mutations_from_vcf {MutationalPatterns}

R Documentation

Retrieve base substitutions from vcf

Description

A function to extract base substitutions of each position in vcf

Usage

mutations_from_vcf(vcf)

Arguments

vcf	A CollapsedVCF object

Value

Character vector with base substitutions

See Also

read_vcfs_as_granges

Examples

## See the 'read_vcfs_as_granges()' example for how we obtained the
## following data:
vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
  package = "MutationalPatterns"
))

muts <- mutations_from_vcf(vcfs[[1]])

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