associations: Query specific variants from specific GWAS
In ieugwasr: Interface to the 'OpenGWAS' Database API

associations

R Documentation

Query specific variants from specific GWAS

Description

Every rsid is searched for against each requested GWAS id. To get a list of available GWAS ids, or to find their meta data, use gwasinfo. Can request LD proxies for instances when the requested rsid is not present in a particular GWAS dataset. This currently only uses an LD reference panel composed of Europeans in 1000 genomes version 3. It is also restricted to biallelic single nucleotide polymorphisms (no indels), with European MAF > 0.01.

Usage

associations(
  variants,
  id,
  proxies = 1,
  r2 = 0.8,
  align_alleles = 1,
  palindromes = 1,
  maf_threshold = 0.3,
  opengwas_jwt = get_opengwas_jwt()
)

Arguments

`variants`	Array of variants e.g. `c("rs234", "7:105561135-105563135")`
`id`	Array of GWAS studies to query. See `gwasinfo` for available studies
`proxies`	`0` or (default) `1` - indicating whether to look for proxies
`r2`	Minimum proxy LD rsq value. Default=`0.8`
`align_alleles`	Try to align tag alleles to target alleles (if `proxies = 1`). `1` = yes (default), `0` = no
`palindromes`	Allow palindromic SNPs (if `proxies = 1`). `1` = yes (default), `0` = no
`maf_threshold`	MAF threshold to try to infer palindromic SNPs. Default = `0.3`.
`opengwas_jwt`	Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.