makeclumps.custom.MAF: Function to make the SNP clumps at different Pvalue cutoffs

In foramashar/fashaR: R package with Foram's functions

Description

Function to make the SNP clumps at different Pvalue cutoffs

Usage

makeclumps.custom.MAF(
  trait,
  clumpfile,
  outfilename,
  MAF = 0.05,
  RSQ = 0.01,
  DIST = 1000,
  plink = F
)

Arguments

trait	Trait to compare SCD results to
clumpfile	File with rsIDs and pvalues for trait of interest. Header MUST be SNP and pvalue
outfilename	Filename for all output files, will be followed by alpha cutoff value
MAF	Maf cutoff to be used for filtering
plink	logical If plink should be used instead of plink2 for clumping. Default (false)

See Also

gtx, grs.plot

foramashar/fashaR documentation built on Nov. 15, 2020, 5:05 a.m.