mut_type_occurrences: Count the occurrences of each base substitution type
In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description Usage Arguments Value See Also Examples

Count the occurrences of each base substitution type

1	mut_type_occurrences(vcf_list, ref_genome)

`vcf_list`	GRangesList or GRanges object.
`ref_genome`	BSGenome reference genome object

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

read_vcfs_as_granges,

## 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)