# tdt.rr: Calculate haplotype relative risks in TDT studies In tdthap: TDT Tests for Extended Haplotypes

## Description

The p-value is the conventional "exact" test based on the binomial distribution of transmissions. The estimated relative risks use a Bayesian method, recommended because of the multiplicity problem. the prior is a beta distribution of the second kind, defined by two "degrees of freedom" parameters. Note that the prior mean is prior.df[1]/prior.df[2] and that Bayes estimates based on small numbers of transmissions are pulled in towards this. A "realistic" choice of these parameters is recommended, and to aid this, the function returns credible intervals using the prior alone as well as the a posteriori interval for each haplotype.

## Usage

 `1` ```tdt.rr(hap, prior.df=c(0.5, 0.5), prob=c(0.05, 0.95)) ```

## Arguments

 `hap` A list containing the transmitted and untransmitted haplotypes. This would normally be computed using `tdt.select`. `prior.df` a vector of length two containing the degree of freedom parameters for the prior distribution of the haplotype relative risk - a beta distribution of the second kind. `prob` The probability levels for Bayesian credibility intervals for the haplotype relative risks.

## Value

A matrix containing the numbers of transmitted and untransmitted haplotypes, the (binomial) p-values, the Bayes estimates of the haplotype relative risks, and the lower and upper bounds of the credible interval. The prior estimate and credible interval is also shown.

## References

Spielman R., McGinnis R., and Ewens, W. (1993) Transmission tests for linkage disequilibrium. American Journal of Human Genetics, 52, 506-16.

`hap.transmit`, `tdt.select`, `tdt.quad`
 ``` 1 2 3 4 5 6 7 8 9 10``` ```## Not run: # Select the sub-haplotype made up from the first two markers and # print tables of TDT tests and haplotype realtaive risks hap.use <- tdt.select(haps, markers=1:2) rr <- tdt.rr(hap.use) rr ## End(Not run) ```