mut_type_occurrences: Count the occurrences of each base substitution type

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

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	GRangesList or GRanges object.
ref_genome	BSgenome reference genome object

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)

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.