Calculate and store linkage test statistics for ALL relative pairs. The tests include
linkage.all(y.mat, x.adj, ibdvar.lst, epsilon=1e-5)
linkage.all.pedloop(y.vec, x.adj, ibdvar.lst)a linkage.all object, containing tests for linkage on all relative pairs
matrix of ibd sharing statistics, the response in the regression model; each column represents one chromosome position.
vector of ibd sharing statistics (at one position), the response in the regression model (pedloop only)
matrix of covariates, x, which are indicators for which status group the relative pairs belong, adjusted by c.scale.
a list containing an element for each pedigree. The elements include ped.id, person1.id, person2.id, and the variance-covariance matrix of pairs of pairs osf subjects.
cutoff for singular values in generalized inverse (Ginv)
linkage.all sets up the linkage calculations for each position, and the calculations are performed over all pedigrees in linkage.all.pedloop.
ibdreg,
print.linkage.all,
plot.linkage.all