get_MAF_UKB: Get MAF from UK Biobank.

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

Get MAF from UK Biobank.

Description

If MAF column is missing, download MAF from UK Biobank and use that instead.

Usage

get_MAF_UKB(
  query_dat,
  output_dir = tools::R_user_dir(package = "echoLD", which = "cache"),
  force_new_maf = FALSE,
  download_method = "axel",
  nThread = 1,
  verbose = TRUE,
  conda_env = "echoR_mini"
)

Arguments

query_dat	SNP-level data.
output_dir	Path to store UKB_MAF file in.
force_new_maf	Download UKB_MAF file again.
download_method	"axel" : Multi-threaded "wget" : Single-threaded "download.file" : Single-threaded "internal" : Single-threaded (passed to download.file) "wininet" : Single-threaded (passed to download.file) "libcurl" : Single-threaded (passed to download.file) "curl" : Single-threaded (passed to download.file)
nThread	Number of threads to parallelize over.
verbose	Print messages.
conda_env	Conda environment to use.

Source

UKB

Examples

query_dat<- echodata::BST1
query_dat$MAF <- NULL
dat2 <- echoLD::get_MAF_UKB(query_dat = query_dat)

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.