adjLD: LD pruning of summary statistics

In qgg: Statistical Tools for Quantitative Genetic Analyses

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".

qgg documentation built on Sept. 8, 2023, 5:52 p.m.