R/clinvaR.R

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

#' clinvaR: collection, analysis, and visualization tools for ClinVar data
#'
#' clinvaR rapidly generates a VCF of annotated variants for a list of genes and 
#' produces simple, ancestry-informed analyses.
#'
#' 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:
#' \itemize{
#' \item  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()
#' \item Download and import relevant variants from 1000 Genomes: 
#' download_1000g(), import_file_1000g().
#' \item Select a version of ClinVar. These can be downloaded directly: download_clinvar(). 
#' Alternatively, ClinVar VCFs before July 2017 can be retrieved locally: get_clinvar().
#' \item 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")`
#'
"_PACKAGE"
#' @import ggplot2 dplyr tidyr seqminer stringr
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