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Obtain top hits from a GWAS dataset

Source: R/query.R
tophits.Rd

By default performs clumping on the server side.

Usage

tophits(
  id,
  pval = 5e-08,
  clump = 1,
  r2 = 0.001,
  kb = 10000,
  pop = "EUR",
  force_server = FALSE,
  opengwas_jwt = get_opengwas_jwt(),
  ...
)

Arguments

id

Array of GWAS studies to query. See gwasinfo for available studies

pval

use this p-value threshold. Default = 5e-8

clump

whether to clump (1) or not (0). Default = 1

r2

use this clumping r2 threshold. Default is very strict, 0.001

kb

use this clumping kb window. Default is very strict, 10000

pop

Super-population to use as reference panel. Default = "EUR". Options are "EUR", "SAS", "EAS", "AFR", "AMR"

force_server

Logical. By default will return preclumped hits. p-value threshold 5e-8, with r2 threshold 0.001 and kb threshold 10000, using only SNPs with MAF > 0.01 in the European samples in 1000 genomes. If force_server = TRUE then will recompute using server side LD reference panel.

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.

...

Unused, for extensibility

Value

Dataframe