linkage.tests: Linkage tests for relative pair groups

Description

Linkage tests, with and without covariates, for relative pair status groups Affected-Affected (AA), Unaffected-Unaffected (UU), or Affected-Unaffected (AU)

Usage

linkage.tests(y.mat, x.adj, ibdvar.lst, status.method, epsilon=1e-5)
linkage.tests.B0(y.mat, xvec, ibdvar.lst)
linkage.tests.pedloop(y.vec, x.adj, ibdvar.lst, 
                      B0, concordant=TRUE, epsilon)

Arguments

y.mat

matrix of ibd sharing statistics, which are the response in the regression model; each column represents one chromosome position.

y.vec

vector of ibd sharing statistics (at one position), which are the response in the regression model (linkage.tests.pedloop only)

x.adj

matrix of covariates, x, adjusted by c.scale.

xvec

the intercept column from x.adj, needed for pre-calculating Beta-0

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 of subjects.

status.method

Character string indicating which relative pairs to apply the linkage tests: "AA", "UU", or "AU".

The intercept in the regression model, ("beta-zero").

concordant

logical; indicate whether to perform tests for linkage on concordant pairs (AA, UU), or discordant (AU).

epsilon

cutoff for singular values in generalized inverse (Ginv)

Value

an object of class linkage.tests

Side Effects

none

Details

The calculations for linkage tests require a pre-calculation of beta-zero (linkage.tests.B0) and then proceed with calculating the linkage test statistics for each position by looping over all pedigrees (linkage.tests.pedloop). Linkage tests can only be applied to one status group at a time, because the tests are restricted to whether the relative pairs are all concordant or discordant. Unexpected allele sharing can be detected when unconstrained linkage > constrained linkage tests. The method also returns z scores for pedigree-specific contributions to unexpected allele sharing indicated in linkage tests.