plotNtdt: A function for plotting the results from ntdt.q

plotNtdtR Documentation

A function for plotting the results from ntdt.q


This function plots the results from ntdt.q


plotNtdt(g, m, alpha = 5e-08, power = 0.8,...)



the genotype risk ratio for the susceptibility gene


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


the Type 1 error rate


the desired power


additional arguments for plot


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.


A plot of the results generated by a call to the ntdt.q() function.


This R program was modeled on Martin Farrall's Mathematica notebook.


Daniel E. Weeks


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

ntdt, ntdt.q


## Duplicate Figures 1 and 2 from Abel and Muller-Myhsok (1998)
## Am J Hum Genet 63:664-667
## gives Figure 1A
## gives Figure 1B

powerpkg documentation built on May 20, 2022, 1:09 a.m.

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