Linkage test statistics for ALL relative pairs

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Description

Calculate and store linkage test statistics for ALL relative pairs. The tests include

Usage

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linkage.all(y.mat, x.adj, ibdvar.lst, epsilon=1e-5)
linkage.all.pedloop(y.vec, x.adj, ibdvar.lst)

Arguments

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)

Details

linkage.all sets up the linkage calculations for each position, and the calculations are performed over all pedigrees in linkage.all.pedloop.

Value

a linkage.all object, containing tests for linkage on all relative pairs

See Also

ibdreg, print.linkage.all, plot.linkage.all

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