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Supply the output from read_exposure_data() and all the SNPs therein will be queried against the requested outcomes in remote database using API.

Source: R/query.R
extract_outcome_data.Rd

Supply the output from read_exposure_data() and all the SNPs therein will be queried against the requested outcomes in remote database using API.

Usage

extract_outcome_data(
  snps,
  outcomes,
  proxies = TRUE,
  rsq = 0.8,
  align_alleles = 1,
  palindromes = 1,
  maf_threshold = 0.3,
  opengwas_jwt = ieugwasr::get_opengwas_jwt(),
  splitsize = 10000,
  proxy_splitsize = 500
)

Arguments

snps

Array of SNP rs IDs.

outcomes

Array of IDs (see id column in output from available_outcomes()).

proxies

Look for LD tags? Default is TRUE.

rsq

Minimum LD rsq value (if proxies = 1). Default = 0.8.

align_alleles

Try to align tag alleles to target alleles (if proxies = 1). 1 = yes, 0 = no. The default is 1.

palindromes

Allow palindromic SNPs (if proxies = 1). 1 = yes, 0 = no. The default is 1.

maf_threshold

MAF threshold to try to infer palindromic SNPs. The default is 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.

splitsize

The default is 10000.

proxy_splitsize

The default is 500.

Value

Dataframe of summary statistics for all available outcomes