powerpkg (version 1.6)

ptb: A power table for the TDT design

Description

Create a power table for different values of q.

Usage

ptb(g, m, ld, nfam, alpha)

Arguments

g

the genotype risk ratio for the susceptibility gene.

m

the frequency of the marker allele in linkage disequilibrium with the susceptibility allele.

ld

the strength ofthe linkage disequilibrium between marker and susceptibility allele, on a scale of 0 to 1.

nfam

the number of families.

alpha

the significance level of the test.

Value

tb

A table of power results as a function of q

Details

We will use an R program that implements the power formulae of Abel and Muller-Myhsok (1998). These formulae allow one to quickly compute power of the TDT approach under a variety of different conditions. This R program was modeled on Martin Farrall's Mathematica notebook.

The power computations here use a simple genetic model with several aspects: (1) The disease locus has two alleles, A and a, with allele frequencies q and 1-q. The risk of disease follows a multiplicative model with genotype relative risks of g and g*g for the A/a and A/A subjects. (2) There is a perfectly linked marker with two alleles, with allele frequencies m and 1-m.

References

Abel L, Muller-Myhsok B. Maximum-likelihood expression of the transmission/disequilibrium test and power considerations. Am J Hum Genet. 1998 Aug;63(2):664-7.

Chen WM, Deng HW. A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes. Genet Epidemiol. 2001 Jul;21(1):53-67.

Iles MM. On calculating the power of a TDT study--comparison of methods. Ann Hum Genet. 2002 Jul;66(Pt 4):323-8.

Purcell S, Cherny SS, Sham PC. Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics. 2003 Jan;19(1):149-50.

See Also

plotNtdt, ntdt.q, ntdt, ptdt

Examples

# NOT RUN {
  ptb(g=1.5,m=0.5,ld=0.75,nfam=2000,alpha=0.00000005)
# }