am_covariance_structure {rBahadur}

Compute Diagonal plus Low Rank equilibrium covariance structure

Description

Compute Diagonal plus Low Rank equilibrium covariance structure

Usage

am_covariance_structure(beta, AF, r)

Arguments

beta

vector of standardized diploid allele-substitution effects

AF

vector of allele frequencies

r

cross-mate phenotypic correlation

Value

Vector 'U' such that $D + U U^T$ corresponds to the expected haploid LD-matrix given the specified genetic architecture (encoded by 'beta' and 'AF') and cross-mate phenotypic correlation 'r'. It is assumed that the total phenotypic variance at generation zero is one.

Examples

set.seed(1)
h2_0 = .5; m = 200; n = 1000; r =.5; min_MAF=.1
betas <- rnorm(m,0,sqrt(h2_0/m))
afs <- runif(m, min_MAF, 1-min_MAF)
output <- am_covariance_structure(betas, afs, r)