Count the occurrences of each base substitution type

Description

Count the occurrences of each base substitution type

Usage

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mut_type_occurrences(vcf_list, ref_genome)

Arguments

vcf_list

A list of CollapsedVCF object

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

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## 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"))

## Exclude mitochondrial and allosomal chromosomes.
autosomal <- extractSeqlevelsByGroup(species="Homo_sapiens",
                                        style="UCSC",
                                        group="auto")

vcfs <- lapply(vcfs, function(x) keepSeqlevels(x, autosomal))

## 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)

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