Extract exposure variables for multivariable MR — mv_extract

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,
  access_token = ieugwasr::check_access_token(),
  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.
access_token: Google OAuth2 access token. Used to authenticate level of access to data.
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
plink_bin: 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