add_gnomAD_AF: Add allele frequencies from gnomAD

In mumichae/tMAE: Tests and visualizes for Mono-allelic expressed variants

Description

Add allele frequency information from gnomAD.

Usage

add_gnomAD_AF(
  data,
  genome_assembly = c("hg19", "hs37d5", "hg38", "GRCh38"),
  max_af_cutoff = 0.001,
  populations = c("AF", "AF_afr", "AF_amr", "AF_eas", "AF_nfe", "AF_popmax"),
  ...
)

Arguments

data	A data.frame containing allelic counts.
genome_assembly	either 'hg19/hs37d5' or 'hg38/GRCh38' indicating the genome assembly of the variants.
max_af_cutoff	cutoff for a variant to be considered rare. Default is .001.
populations	The population to be annotated.
...	Used for backwards compatibility (gene_assembly -> genome_assembly)

Value

A data.table with the original contents plus columns containing allele frequencies from different gnomAD populations.

Author(s)

Vicente Yepez

Examples

file <- system.file("extdata", "allelic_counts_HG00187.csv", package = "tMAE", mustWork = TRUE)
maeCounts <- fread(file)
maeRes <- DESeq4MAE(maeCounts)
maeRes <- add_gnomAD_AF(maeCounts, genome_assembly = 'hg19', pop="AF")

mumichae/tMAE documentation built on Oct. 11, 2021, 11:41 p.m.