CovarMatrix: Calculation of covariance matrices from maternal and paternal...
In hscovar: Calculation of Covariance Between Markers for Half-Sib Families

Description Usage Arguments Details Value Examples

The covariance matrix is set as maternal plus paternal LD matrix where the paternal part is a weighted average of sire-specific LD matrices.

1	CovarMatrix(exp_freq_mat, LDDam, LDSire, Ns)

`exp_freq_mat`	[MATRIX] paternal EXPECTATION matrix
`LDDam`	[MATRIX] maternal Linkage Disequilibrium matrix
`LDSire`	[LIST] Linkage disequilibrium matrices for the sires; each element of the list corresponds to a family
`Ns`	[VECTOR] family size for each sire s

The internal suMM function works on lists!

covK: (p x p) matrix of covariance between markers

 data(testdata)
 G <- Haplo2Geno(H.sire)
 E <- ExpectMat(G)
 LDfam2 <- LDsire(H.sire, pos.chr, family = 3:4)
 LDfam3 <- LDsire(H.sire, pos.chr, family = 5:6)
 ## covariance matrix based on sires 2 and 3 only, each with 100 progeny
 K <- CovarMatrix(E[2:3, ], LDDam = matLD, LDSire = list(LDfam2, LDfam3), Ns = c(100, 100))