import.trinucleotides.counts: import.trinucleotides.counts

In SparseSignatures: SparseSignatures

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)

SparseSignatures documentation built on Nov. 8, 2020, 4:55 p.m.