README.md

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

clinvaR

R Package: annotated gene-level VCFs and ancestry-informed analyses from ClinVar data.

Purpose

The goal of clinvaR is to quickly generate a VCF of annotated variants relevant to a list of genes, and produce simple, ancestry-informed analyses.

Installation

# install.packages("devtools")
devtools::install_github("jamesdiao/clinvaR")
require(clinvaR)

Usage

To acquire a VCF with the July 5, 2017 ClinVar file and all default settings, simply run annotate(genes).

More specific modifications can be made by changing the 4 steps:

1. Select a list of genes that you are interested in. This can be done by manual input, by importing a .tsv from MacArthur's gene lists (stored locally), or by importing your own .tsv file: get_genes()
2. Download and import relevant variants from 1000 Genomes: download_1000g(), import_file_1000g().
3. Select a version of ClinVar. These can be downloaded directly: download_clinvar(). Alternatively, ClinVar VCFs before July 2017 can be retrieved locally: get_clinvar().
4. Use the ClinVar file to annotate the gene-level variant VCF: annotate_1000g().

clinvaR also provides a few basic analysis and visualization functions that can be run directly : freq_over_time, var_plot_1000g.

James Diao | Arjun Manrai | Kohane Lab | 07/27/2017

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