dot-read_dataset: Read datasets

In jwr-git/mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

Read datasets

Description

Helper function that is called from read_exposure and read_outcome. Extracts exposure and outcome data according to arguments. Should not be called directly.

Usage

.read_dataset(
  ids,
  rsids = NULL,
  pval = 5e-08,
  proxies = TRUE,
  proxy_rsq = 0.8,
  proxy_kb = 5000,
  proxy_nsnp = 5000,
  plink = NULL,
  bfile = NULL,
  clump_r2 = 0.01,
  clump_kb = 10000,
  pop = "EUR",
  type = "exposure",
  cores = 1,
  cores_proxy = 1,
  verbose = TRUE
)

Arguments

ids	List of OpenGWAS IDs or file paths (to gwasvcf files)
rsids	List of SNP rsIDs to extract
pval	Threshold to extract SNPs (Optional)
proxies	Whether to search for proxies (Optional, boolean)
proxy_rsq	R2 threshold to use when searching for proxies (Optional)
proxy_kb	kb threshold to use when searching for proxies (Optional)
proxy_nsnp	Number of SNPs when searching for proxies (Optional)
plink	Path to Plink binary (Optional)
bfile	Path to Plink .bed/.bim/.fam files (Optional)
clump_r2	r2 threshold for clumping SNPs (Optional)
clump_kb	Distance outside of which SNPs are considered in linkage equilibrium (Optional)
pop	Population (Optional, used only for clumping on OpenGWAS)
type	Type of data (Optional, "exposure" or "outcome")
cores	Number of cores for multi-threaded tasks (Optional) NB: Unavailable on Windows machines
cores_proxy	Number of cores for multi-threaded proxy searching (Optional) NB: Unavailable on Windows machines NB: Should not be more than 'cores' argument!
verbose	Display verbose information (Optional, boolean)

Value

Data.frame of datasets

See Also

[read_exposure()], [read_outcome()]

jwr-git/mrpipeline documentation built on Oct. 2, 2022, 3:41 p.m.