extract_outcome_data: Supply the output from 'read_exposure_data()' and all the...

In MRCIEU/TwoSampleMR: Two Sample MR Functions and Interface to MR Base Database

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

Description

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

MRCIEU/TwoSampleMR documentation built on Sept. 28, 2024, 6:51 p.m.