vargen_install: Download the files needed to run 'vargen_pipeline'

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Download the files needed to run vargen_pipeline

Description

Only need to run it once. Will download the following files in "install_dir":

• the latest gwas catalog, eg: gwas_catalog_v1.0.2-associations_e93_r2019-01-11.tsv

• hg19ToHg38.over.chain.gz (will be unzipped)

• GTEx_Analysis_v8_eQTL.tar.gz (will be untared)

• GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.lookup_table.txt.gz

• enhancer_tss_associations.bed

Usage

vargen_install(
  install_dir = "./",
  gtex_version = "v8",
  timeout = 10000,
  verbose = FALSE
)

Arguments

install_dir	the path to the installation folder (default = "./")
gtex_version	the version of gtex to download, only "v7" and "v8" are supported (default = "v8")
timeout	the timeout set in options(), reading/downloading files online might fail with the default timeout of 60 seconds.
verbose	if TRUE will print progress messages (default = FALSE)

Value

nothing, download files in "install_dir".

Examples

vargen_install("./", verbose = TRUE)

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.