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]])


[Package MutationalPatterns version 2.0.0 Index]