ld_clump_api: Perform clumping on the chosen variants using through API

View source: R/ld_clump.R

ld_clump_apiR Documentation

Perform clumping on the chosen variants using through API

Description

Perform clumping on the chosen variants using through API

Usage

ld_clump_api(
  dat,
  clump_kb = 10000,
  clump_r2 = 0.1,
  clump_p,
  pop = "EUR",
  access_token = check_access_token(),
  opengwas_jwt = get_opengwas_jwt()
)

Arguments

dat

Dataframe. Must have a variant name column (variant) and pval column called pval. If id is present then clumping will be done per unique id.

clump_kb

Clumping kb window. Default is very strict, 10000

clump_r2

Clumping r2 threshold. Default is very strict, 0.001

clump_p

Clumping sig level for index variants. Default = 1 (i.e. no threshold)

pop

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

access_token

Google OAuth2 access token. Used to authenticate level of access to data. By default, checks if already

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.#' @param bfile If this is provided then will use the API. Default = NULL

Value

Data frame of only independent variants


MRCIEU/ieugwasr documentation built on April 20, 2024, 11:31 p.m.