download_vcf: Download VCF file and its index file from Open GWAS

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Download VCF file and its index file from Open GWAS

Description

Ideally, we would use gwasvcf instead but it hasn't been made available on CRAN or Bioconductor yet, so we can't include it as a dep.

Usage

download_vcf(
  vcf_url,
  vcf_dir = tempdir(),
  vcf_download = TRUE,
  download_method = "download.file",
  force_new = FALSE,
  quiet = FALSE,
  timeout = 10 * 60,
  nThread = 1
)

Arguments

vcf_url	Remote URL to VCF file.
vcf_dir	Where to download the original VCF from Open GWAS. WARNING: This is set to tempdir() by default. This means the raw (pre-formatted) VCFs be deleted upon ending the R session. Change this to keep the raw VCF file on disk (e.g. vcf_dir="./raw_vcf").
vcf_download	Download the original VCF from Open GWAS.
download_method	"axel" (multi-threaded) or "download.file" (single-threaded) .
force_new	Overwrite a previously downloaded VCF with the same path name.
quiet	Run quietly.
timeout	How many seconds before giving up on download. Passed to download.file. Default: 10*60 (10min).
nThread	Number of threads to parallelize over.

Value

List containing the paths to the downloaded VCF and its index file.

Examples

#only run the examples if user has internet access:
if(try(is.character(getURL("www.google.com")))==TRUE){
vcf_url <- "https://gwas.mrcieu.ac.uk/files/ieu-a-298/ieu-a-298.vcf.gz"
out_paths <- download_vcf(vcf_url = vcf_url)
}

neurogenomics/MungeSumstats documentation built on July 17, 2024, 3:14 p.m.