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 1.2.0 Index]