load_recurrent_mutations: Load File with Recurrent Mutations to exclude

In andygxzeng/ECSI: Espresso - Somatic Mutation Calling using Contextual Error Models

Description

Loads in recurrent mutations from tab or comma-delimited file with four columns (Chr, Pos, Ref, Alt) and no header, presenting it as a VRanges file.

Usage

load_recurrent_mutations(file, genome)

Arguments

file	Location of file with recurrent mutations
genome	Reference genome to use

Value

This function returns a VRanges object including:

• seqnames

• ranges

• ref

• alt

Examples

## Not run: 
recurrent <- load_recurrent_mutations(file = "COSMIC_Heme_mutations_freq10.txt", genome)

## End(Not run)

andygxzeng/ECSI documentation built on Feb. 6, 2021, 8:53 a.m.