R Package: annotated gene-level VCFs and ancestry-informed analyses from ClinVar data.
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.
# install.packages("devtools")
devtools::install_github("jamesdiao/clinvaR")
require(clinvaR)
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:
get_genes()
download_1000g(), import_file_1000g()
. download_clinvar()
. Alternatively, ClinVar VCFs before July 2017 can be retrieved locally: get_clinvar()
.annotate_1000g()
.clinvaR
also provides a few basic analysis and visualization functions that can be run directly : freq_over_time
, var_plot_1000g
.
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