annotate_1000g: Annotate 1000 Genomes Variant VCF using ClinVar

In jamesdiao/clinvaR: collection, analysis, and visualization tools for ClinVar data

Description

This function takes a merged ClinVar-sequencing dataset and returns an ancestry-stratified plot of allele frequencies.

Usage

annotate_1000g(vcf)
annotate_1000g(genes)
annotate_1000g(vcf, conflicts = FALSE)

Arguments

vcf	data.frame; clinvaR-processed vcf containing 1000 genomes sequencing data. Defaults to importing data from all downloads: vcf <- import_file_1000g().
clinvar	data.frame; clinvaR-processed vcf containing ClinVar data. Defaults to get_clinvar().

Examples

annotate_1000g(genes = get_genes())
annotate_1000g(clinvar = get_clinvar(), vcf = import_file_1000g())

jamesdiao/clinvaR documentation built on May 18, 2019, 11:19 a.m.