import.trinucleotides.counts {SparseSignatures} | R Documentation

## import.trinucleotides.counts

### Description

Make trinucleotides counts matrix from input data for a given reference genome.

### Usage

    import.trinucleotides.counts(data, reference = NULL)

### Arguments

`data` | a data.frame with variants having 6 columns: sample name, chromosome, start position, end position, ref, alt.
`reference` | a BSgenome object with the reference genome to be used to retrieve flanking bases.

### Value

A matrix with trinucleotides counts per patient.

### Examples

    ## Not run:
    data(ssm560_reduced)
    library("BSgenome.Hsapiens.1000genomes.hs37d5")
    trinucleotides_counts = import.trinucleotides.counts(data=ssm560_reduced,
         reference=BSgenome.Hsapiens.1000genomes.hs37d5)

    ## End(Not run)

[Package SparseSignatures version 2.2.0 Index]