mut_type_occurrences {MutationalPatterns}R Documentation

Count the occurrences of each base substitution type

Description

Count the occurrences of each base substitution type

Usage

mut_type_occurrences(vcf_list, ref_genome)

Arguments

vcf_list

A GRangesList

ref_genome

Reference genome

Value

data.frame with counts of each base substitution type for each sample in vcf_list

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"))

## Load a reference genome.
ref_genome = "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)

## Get the type occurrences for all VCF objects.
type_occurrences = mut_type_occurrences(vcfs, ref_genome)


[Package MutationalPatterns version 1.12.0 Index]