ld_clump_api: Perform clumping on the chosen variants using through API

Description Usage Arguments

View source: R/ld_clump.R

Description

Perform clumping on the chosen variants using through API

Usage

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

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#' @return Data frame of only independent variants


MRCIEU/ieugwasr documentation built on May 8, 2021, 4:18 a.m.