import_file_1000g: Imports downloaded VCF from 1000 Genomes

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

Description

This function imports a gene's VCF and extracts attributes from INFO into a specified format for other clinvaR analyses

Usage

import_file_1000g(genes, dataset, path)

Arguments

gene	character; any of the pre-stored genes in extdata/1000G Not case-sensitive. Defaults to 'gnomAD'.
path	character; path to an importable VCF. Overrides gene input.

Examples

import_file_1000g('BRCA2')
ACMG.1000g <- NULL
for (gene in ACMG.panel) {
ACMG.1000g <- rbind(ACMG.1000g,import_file_1000g(gene))
}
#ACMG.1000g[duplicated(ACMG.1000g$VAR_ID),1:8] # Display and remove duplicates
ACMG.1000g <- ACMG.1000g[!duplicated(ACMG.1000g$VAR_ID),]

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