mut_type: Retrieve base substitution types from a VCF object

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Retrieve base substitution types from a VCF object

Description

A function to extract the base substitutions from a vcf and translate to the 6 common base substitution types.

Usage

mut_type(vcf)

Arguments

vcf	A CollapsedVCF object

Value

Character vector with base substitution types

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"
))

mut_type(vcfs[[1]])

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.