Implementation of Z matrix #6
Description
It is difficult to understand from documentation whether the Z matrix parameter is used and cofactors can be used in the modelling. The following suggests that the expectation is that the phenotype matrix contains a single row per genotype.
if(is.null(Z)){
Z<-diag(nrow(phenotypes))
}
The map.QTL function documentation states:
"Not updated for vector phenotypes yet."
Does this imply that observations y in the phenotype matrix represent a single observation per genotype and not multiple observations?
The documentation for Z parameter states:
" For instance, if multiple samples correspond to the same
#' individual, this matrix should indicate so."
Is this implying that the matrix is addressing the case where multiple genotyping samples have been taken from a given individual or that y can comprise multiple observations (say over years, sites etc) per individual genotype?