read_exposure: Read exposures

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

Read exposures

Description

Read a dataset (or datasets) as exposure. Can accept both OpenGWAS IDs or file paths. Accepts only gwasvcf file formats. This function can clump data locally, if supplied with the 'plink' and 'bfile' arguments. If these are not supplied, clumping will take place on the OpenGWAS servers only for OpenGWAS IDs. If you would like to clump local files, please provide paths to Plink and bfiles.

Usage

read_exposure(
  ids,
  pval = 5e-08,
  plink = NULL,
  bfile = NULL,
  clump_r2 = 0.01,
  clump_kb = 10000,
  pop = "EUR",
  cores = 1,
  verbose = TRUE
)

Arguments

ids	List of OpenGWAS IDs or file paths (to gwasvcf files)
pval	Threshold to extract SNPs (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)
cores	Number of cores for multi-threaded tasks (Optional) NB: Unavailable on Windows machines
verbose	Display verbose information (Optional, boolean)

Value

Data.frame of exposure datasets

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