clinvaR-package: clinvaR: collection, analysis, and visualization tools for...

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

Description

clinvaR rapidly generates a VCF of annotated variants for a list of genes and produces simple, ancestry-informed analyses.

Details

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:

• 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()

• Download and import relevant variants from 1000 Genomes: download_1000g(), import_file_1000g().

• Select a version of ClinVar. These can be downloaded directly: download_clinvar(). Alternatively, ClinVar VCFs before July 2017 can be retrieved locally: get_clinvar().

• 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. To learn more about clinvaR, start with the vignettes: 'browseVignettes(package = "clinvaR")'

Author(s)

Maintainer: James Diao [e-mail]

Other contributors:

• Arjun Manrai [e-mail] [thesis advisor]

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