qgg (version 1.1.1)

adjLD: LD pruning of summary statistics

Description

Perform LD pruning of summary statistics before they are used in gene set enrichment analyses.

Usage

adjLD(
  stat = NULL,
  Glist = NULL,
  chr = NULL,
  statistics = "p-value",
  r2 = 0.9,
  ldSets = NULL,
  threshold = 1,
  method = "pruning"
)

Arguments

stat

a data frame with marker summary statistics (see required format above)

Glist

list of information about genotype matrix stored on disk

chr

chromosome(s) being processed

statistics

specificy what type of statistics ("b" or "z") is being processed (default is "b")

r2

threshold used in clumping/pruning procedure (default is 0.9)

ldSets

list of marker sets - names corresponds to row names in stat

threshold

p-value threshold used in LD pruning

method

method used in adjustment for linkage disequilibrium (default is "clumping")