adjLD

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

stat

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

statistics

list providing information about genotypes stored on disk

Glist

threshold for r2 used in LD pruning

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

ldSets

p-value threshold used in LD pruning

threshold

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

method

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

Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses.
Rohde et al. (2019) <doi:10.1101/503631>.

adjLD: LD pruning of summary statistics

Description

Usage

Arguments