annotate_MAF: Annotate MAF

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

Description

Annotate VRanges object with population minor allele frequency from gnomAD

Usage

annotate_MAF(sample, MAF_database, genome)

Arguments

sample	VRanges object of the varscan pileup2cns output
MAF_database	GScores object with MAFs for each position
genome	Genome of input object, accepts either hg19 or hg38

Value

This function returns the VRanges object with the additional metadata column MAF.

Examples

## Not run: 
# Sample with hg19 reference, annotated with gnomAD exome hs37d5
variants <- load_as_VRanges(sample_name = "pt123",
    sample_path = "./patient_123_pileup2cns", genome = "hg19", metadata = TRUE)
library(MafDb.gnomADex.r2.1.hs37d5)
variants <- annotate_MAF(sample = variants,
    MAF_database = MafDb.gnomADex.r2.1.hs37d5, genome = "hg19")

## End(Not run)
## Not run: 
# Sample with hg38 reference, annotated with gnomAD genome GRCh38
variants <- load_as_VRanges(sample_name = "pt321",
    sample_path = "./patient_321_pileup2cns", genome = "hg38", metadata = TRUE)
library(MafDb.gnomAD.r2.0.1.GRCh38)
variants <- annotate_MAF(sample = variants,
    MAF_database = MafDb.gnomAD.r2.0.1.GRCh38, genome = "hg38")

## End(Not run)

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