calc_Sigma

d by d genetic covariance matrix for the d phenotypes

d by d error covariance matrix for the d phenotypes

optional n by n kinship matrix. if NULL, Vg is not used.

kinship

n_mouse

Calculate the phenotypes covariance matrix Sigma

We implement an
adaptation of Jiang & Zeng's (1995) <https://www.genetics.org/content/140/3/1111> likelihood ratio test for testing
the null hypothesis of pleiotropy against the alternative hypothesis,
two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) <https://www.genetics.org/content/140/3/1111>
and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in
that our test accommodates multiparental populations.

calc_Sigma: Calculate the phenotypes covariance matrix Sigma

Description

Usage

Arguments

Value