linkage.all | R Documentation |
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)
y.mat |
matrix of ibd sharing statistics, the response in the regression model; each column represents one chromosome position. |
y.vec |
vector of ibd sharing statistics (at one position), the response in the regression model (pedloop only) |
x.adj |
matrix of covariates, x, which are indicators for which status group the relative pairs belong, adjusted by c.scale. |
ibdvar.lst |
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. |
epsilon |
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.
a linkage.all object, containing tests for linkage on all relative pairs
ibdreg
,
print.linkage.all
,
plot.linkage.all
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