mut_matrix {MutationalPatterns} | R Documentation

## Make mutation count matrix of 96 trinucleotides

### Description

Make 96 trinucleotide mutation count matrix

### Usage

    mut_matrix(vcf_list, ref_genome)

### Arguments

`vcf_list` | List of collapsed vcf objects
`ref_genome` | BSGenome reference genome object

### Value

96 mutation count matrix

### 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 the corresponding reference genome.
    ref_genome = "BSgenome.Hsapiens.UCSC.hg19"
    library(ref_genome, character.only = TRUE)

    ## Construct a mutation matrix from the loaded VCFs in comparison to the
    ## ref_genome.
    mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome)

[Package MutationalPatterns version 1.99.3 Index]