calc_covs: Calculate Vg and Ve from d-variate phenotype and kinship

In qtl2pleio: Testing Pleiotropy in Multiparental Populations

Description

Calculate Vg and Ve from d-variate phenotype and kinship

Usage

calc_covs(
  pheno,
  kinship,
  X1pre = rep(1, nrow(kinship)),
  max_iter = 1e+06,
  max_prec = 1/1e+08,
  covariates = NULL
)

Arguments

pheno	n by d matrix of phenotypes
kinship	a kinship matrix, n by n
X1pre	n by c design matrix. c = 1 to ignore genotypes
max_iter	maximum number of EM iterations
max_prec	maximum precision for stepwise increments in EM algorithm
covariates	a n by n.cov matrix of numeric covariates

Value

a list with 2 named components, Vg and Ve. Each is a d by d covariance matrix.

Examples

calc_covs(pheno = matrix(data = rnorm(100), nrow = 50, ncol = 2), kinship = diag(50))

qtl2pleio documentation built on Dec. 3, 2020, 1:06 a.m.