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

 tdt.rr R Documentation

## Calculate haplotype relative risks in TDT studies

### 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

```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`

### Examples

```## 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)```

tdthap documentation built on Oct. 29, 2022, 1:14 a.m.