qgg (version 1.1.2)

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. Ensure that it is in the correct format.

Glist

List of information about the genotype matrix stored on disk.

chr

Chromosome(s) being processed.

statistics

Specify what type of statistics ("b", "z", or "p-value") is being processed. Default is "p-value".

r2

Threshold used in the clumping/pruning procedure. Default is 0.9.

ldSets

List of marker sets - names correspond to row names in `stat`.

threshold

P-value threshold used in LD pruning.

method

Method used in adjustment for linkage disequilibrium. Options are "pruning" or "clumping". Default is "pruning".