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 1.4.3 Index]