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, extension = 1)

### Arguments

`vcf_list` | GRangesList or GRanges object.
`ref_genome` | BSGenome reference genome object
`extension` | The number of bases, that's extracted upstream and downstream of the base substitutions. (Default: 1).

### 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:
    grl <- 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 = grl, ref_genome = ref_genome)

    ## Construct a mutation matrix with a larger context.
    ## This is most usefull when you have many mutations per sample.
    mut_mat_extended <- mut_matrix(vcf_list = grl, ref_genome = ref_genome, extension = 2)

[Package MutationalPatterns version 3.0.1 Index]