download.datasets: Download some useful datasets

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Description

Download some useful datasets. Some functions such as plotting and fasta querying require additional data.

Usage

download.datasets(datasets = "all", data.dir = paste0(Sys.getenv("HOME"), "/bedr/data"))

Arguments

datasets	A list of datasets to download. Defaults to "all" i.e. c("refgene","hg19","b37","hugo", "cosmic","clinvar")
data.dir	A directory to put the data. Defaults to ~/bedr/data

Details

External datasets are required for some bedr functionality. For example, plotting intersections based on genes, get.fasta, bed2vcf and validate.gene.names. If these datasets already exist you can simply place symlinks in a directory and use bedr.setup() to define the data.dir.

Value

some datasets.

Author(s)

Daryl Waggott

Examples

## Not run: 
  download.datasets("cosmic");
  
## End(Not run)

bedr documentation built on May 2, 2019, 11:36 a.m.