pathwas_ld_clump_local: Wrapper for clump function using local plink binary and ld...

In Sabor117/PathWAS: Creates predictive models of biological pathway functionality

Wrapper for clump function using local plink binary and ld reference dataset

Description

Wrapper for clump function using local plink binary and ld reference dataset

Usage

pathwas_ld_clump_local(
  dat,
  clump_kb,
  clump_r2,
  clump_p,
  bfile,
  plink_bin,
  def_tmpDir
)

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)
bfile	If this is provided then will use the API. Default = 'NULL'
plink_bin	Specify path to plink binary. Default = 'NULL'. See https://github.com/explodecomputer/plinkbinr for convenient access to plink binaries

Value

data frame of clumped variants

Sabor117/PathWAS documentation built on Nov. 29, 2024, 7:44 a.m.