MphEM {gemma2}

Perform expectation-maximization algorithm to infer Vg and Ve values for a pair of traits.

Description

Perform expectation-maximization algorithm to infer Vg and Ve values for a pair of traits.

Usage

MphEM(
  max_iter = 10000,
  max_prec = 1/1e+06,
  eval,
  X,
  Y,
  V_g,
  V_e,
  verbose_output = FALSE
)

Arguments

max_iter

maximum number of iterations for EM algorithm

max_prec

maximum precision for EM algorithm

eval

vector of eigenvalues from relatedness matrix decomposition

X

design matrix. Typically contains founder allele dosages.

Y

matrix of phenotype values

V_g

genetic covariance matrix

V_e

error covariance matrix

verbose_output

logical indicating whether to output entire collection of intermediate values for all iterations. Default is FALSE.

Value

a list of lists. Length of list corresponds to number of EM iterations