Set similarity function for Geary-Moran type TDT tests

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Description

Haplotypes are only similar if they are IBS at the focal locus. The extent of the similar region to each side is determined by stepping outwards until the haplotypes are no longer IBS, the region being assumed to end midway between the last IBS locus and the first non-IBS locus. If the haplotypes are IBS at the last locus, half the "off-end" distance is scored. The similarity is defined as the total length of this shared region raised to some power.

Usage

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set.similarity(nloci=1, spacing=rep(1, nloci + 1), focus=1, power=1)

Arguments

nloci

The number of loci.

spacing

A numeric array of length (nloci+1) giving marker spacings and "off-end" distances.

focus

An integer in the range 1:nloci indicating the "focus" for the similarity function.

power

The power to which the shared haplotype length is raised.

Value

A list of the values loaded.

Side Effects

Sets constants accessed by tdt.quad() when calculating Geary-Moran type statistics.

References

Clayton, D. and Jones, H. (1999) Transmission/disequilibrium tests for extended marker haplotypes. Am.J.Hum.Gen., 65:1161-1169.

See Also

tdt.quad, get.similarity

Examples

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## Not run: 
# To do a Geary_Moran test on a 10 marker haplotype
	gaps <- c(0, 50, 60, 80, 20, 30, 50, 40, 50, 100, 0)
	set.similarity(nloci=10, spacing=gaps, power=0.5)
	test <- tdt.quad(hap.use, funct=T)

## End(Not run)