import.counts.data {SparseSignatures} | R Documentation

## import.counts.data

### Description

Import point mutations data to build the count matrix to extract mutatational signatues.

### Usage

    import.counts.data(input, bsg, mutation_categories)

### Arguments

`input` | either a data.frame/data.table object or a file with 5 columns: sample name, chromosome, position, ref, alt.
`bsg` | a BSgenome object for the reference genome. Chromosome names have to match the input table.
`mutation_categories` | array with the 96 mutational categories to be considered. It is provided along with the package by data(mutation_categories).

### Value

A count matrix to extract mutatational signatues

### Examples

    data(ssm560_reduced)
    library("BSgenome.Hsapiens.1000genomes.hs37d5")
    bsg = BSgenome.Hsapiens.1000genomes.hs37d5
    data(mutation_categories)
    imported_data = import.counts.data(input=ssm560_reduced,bsg=bsg,mutation_categories=mutation_categories)

[Package SparseSignatures version 1.6.0 Index]