download_vcf {MungeSumstats} | R Documentation |
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.
download_vcf( vcf_url, vcf_dir = tempdir(), vcf_download = TRUE, download_method = "download.file", force_new = FALSE, quiet = TRUE, nThread = 1 )
vcf_url |
Remote URL to VCF file. |
vcf_dir |
Where to download the original VCF from Open GWAS.
WARNING: This is set to |
vcf_download |
Download the original VCF from Open GWAS. |
download_method |
|
force_new |
Overwrite a previously downloaded VCF with the same path name. |
quiet |
Run quietly. |
nThread |
Number of threads to parallelize over. |
List containing the paths to the downloaded VCF and its index file.
#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) }