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Extract exposure variables for multivariable MR

Source: R/multivariable_mr.R
mv_extract_exposures.Rd

Requires a list of IDs from available_outcomes. For each ID, it extracts instruments. Then, it gets the full list of all instruments and extracts those SNPs for every exposure. Finally, it keeps only the SNPs that are a) independent and b) present in all exposures, and harmonises them to be all on the same strand.

Usage

mv_extract_exposures(
  id_exposure,
  clump_r2 = 0.001,
  clump_kb = 10000,
  harmonise_strictness = 2,
  opengwas_jwt = ieugwasr::get_opengwas_jwt(),
  find_proxies = TRUE,
  force_server = FALSE,
  pval_threshold = 5e-08,
  pop = "EUR",
  plink_bin = NULL,
  bfile = NULL
)

Arguments

id_exposure

Array of IDs (e.g. c(299, 300, 302) for HDL, LDL, trigs)

clump_r2

The default is 0.01.

clump_kb

The default is 10000.

harmonise_strictness

See the action option of harmonise_data(). The default is 2.

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.

find_proxies

Look for proxies? This slows everything down but is more accurate. The default is TRUE.

force_server

Whether to search through pre-clumped dataset or to re-extract and clump directly from the server. The default is FALSE.

pval_threshold

Instrument detection p-value threshold. Default = 5e-8

pop

Which 1000 genomes super population to use for clumping when using the server

If NULL and bfile is not NULL then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL

bfile

If this is provided then will use the API. Default = NULL

Value

data frame in exposure_dat format