make_TwoSampleMR_dat: Create a harmonised dataset from lists of vcf files

In MRCIEU/gwasglue: GWAS summary data sources connected to analytical tools

Description

This mimics the TwoSampleMR::make_dat function, which automatically looks up exposure and outcome datasets and harmonises them, except this function uses GWAS-VCF datasets instead. The supporting reference datasets can be accessed by UoB users on BC4 using set_bc4_files()

Usage

make_TwoSampleMR_dat(
  id1,
  id2,
  proxies = TRUE,
  nthreads = 1,
  vcfdir = options()$gwasglue.vcfdir,
  proxydb = options()$gwasglue.proxydb,
  rsidx = options()$gwasglue.rsidx,
  bfile = options()$gwasglue.bfile,
  action = 1,
  plink_bin = genetics.binaRies::get_plink_binary()
)

Arguments

id1	Exposure datasets. Either an array of vcf files, or array of IDs if vcfdir is set
id2	Outcome datasets. Either an array of vcf files, or array of IDs if vcfdir is set
proxies	Lookup proxies? default=TRUE but requires either bfile or proxydb to be set
nthreads	Parellelise default=1
vcfdir	Location of vcf files if id1 and id2 are just IDs. Defaults to options()$gwasglue.vcfdir
proxydb	Location of LD proxy database Default=options()$gwasglue.proxydb
rsidx	Location of rsidx index database Default=options()$gwasglue.rsidx
bfile	Location of LD reference panel Default=options()$gwasglue.bfile

Value

harmonised dataset

MRCIEU/gwasglue documentation built on Feb. 15, 2022, 3:25 p.m.