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qgg (version 1.0.4)

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

Arguments

stat

vector or matrix of single marker statistics (e.g. coefficients, t-statistics, p-values)

statistics

is the type of statistics used in stat (e.g. statistics="p-value")

Glist

list providing information about genotypes stored on disk

r2

threshold for r2 used in LD pruning

ldSets

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

threshold

p-value threshold used in LD pruning

method

used including method="pruning" which is default or "clumping"