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()
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() )
| 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 |
harmonised dataset