mut_type {MutationalPatterns}R Documentation

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]])


[Package MutationalPatterns version 1.8.0 Index]