This function searches for GWAS significant SNPs (for a given p-value) for a specified set of outcomes. It then performs LD based clumping to return only independent significant associations.

extract_instruments(
outcomes,
p1 = 5e-08,
clump = TRUE,
p2 = 5e-08,
r2 = 0.001,
kb = 10000,
access_token = ieugwasr::check_access_token(),
force_server = FALSE
)

## Arguments

outcomes Array of outcome IDs (see available_outcomes). Significance threshold. The default is 5e-8. Logical; whether to clump results. The default is TRUE. Secondary clumping threshold. The default is 5e-8. Clumping r2 cut off. The default is 0.001. Clumping distance cutoff. The default is 10000. Google OAuth2 access token. Used to authenticate level of access to data. The default is ieugwasr::check_access_token(). Force the analysis to extract results from the server rather than the MRInstruments package.

data frame