rres (version 1.1)

ld.weights: LD weights

Description

ld.weights computes LD weights for all markers, which is subsequently used to compute LD weighted GRM.

Usage

ld.weights(data, input.genotype = TRUE)

Arguments

data

numeric matrix.

input.genotype

logical.

Value

A numeric vector of weights. Note that the sum of weights is not constrained to be 1. They should be scaled appropriately before computing the LD weighted GRM.

Details

data can either be the subject by marker numeric genotype matrix (with 0, 1 or 2 coding), or the matrix of marker genotypic correlations. The default option is to input genotype matrix.

Examples

# NOT RUN {
# simulate genotypes of 500 individuals at 100 markers
nsnp = 100 # number of SNPs
freq = runif(nsnp, 0.05, 0.95)
nhaplo = 1000 # number of founder haplotypes
haplo.mat = sim.haplotype(freq, nhaplo)
geno.mat = t(sapply(c(1:500), function(x) 4 - haplo.mat[2*x-1,] - haplo.mat[2*x,]))

# compute unconstrained LD weights
ld.weights(geno.mat)
# }