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Count SNV Contexts

Source: R/mutationalpatterns.R
sig_count_snv.Rd

Counts SNV Contexts.

Usage

sig_count_snv(vcf_gr, ref_genome)

Arguments

vcf_gr

GRanges containing all mutation types from a single sample.

ref_genome

The BSGenome reference genome to use.

Value

A list with two elements:

  • snv_counts: matrix containing the number of SNVs per COSMIC context per gr.

  • gr_snv: GRanges object containing the SNVs.