# HWExactPrevious: Exact test for Hardy-Weinberg equilibrium In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

 HWExactPrevious R Documentation

## Exact test for Hardy-Weinberg equilibrium

### Description

`HWExactPrevious` performs an exact test for Hardy-Weinberg equilibrium

### Usage

```HWExactPrevious(X, alternative = "two.sided", pvaluetype = "selome",
x.linked = FALSE, verbose = FALSE)
```

### Arguments

 `X` vector with the genotype counts AA, AB, BB `alternative` `two.sided` (default) will perform a two-sided test where both an excess and a dearth of heterozygotes count as evidence against HWE. `less` is a one-sided test where only dearth of heterozygotes counts a evidence against HWE, `greater` is a one-sided test where only excess of heterozygotes counts as evidence against HWE. `pvaluetype` if `pvaluetype` is set to `dost` then the p-value of a two-sided test is computed as twice the tail area of a one-sided test. When set to `selome`, the p-value is computed as the sum of the probabilities of all samples less or equally likely as the current sample. When set to `midp`, the p-value is computed as half the probability of the current sample + the probabilities of all samples that are more extreme. `x.linked` `x.linked=FALSE` indicates the marker is autosomal (default), and `x.linked=TRUE` indicates it resides on the X-chromosome. `verbose` print results or not.

### Details

`HWExactPrevious` uses the recursion equations described by Wigginton et. al.

For large samples, `HWExactPrevious` may give the error message: "evaluation nested too deeply: infinite recursion". This can usually be resolved by increasing R's limit on nested expressions with `options(expressions=10000)` or a higher limit. With higher limits, the error message "protect(): protection stack overflow" can occur. This error can usually be resolved by increasing R's protection stack with the command line option `--max-ppsize 100000` or higer values. However, with such large samples the exact test will give virtually the same result as a chi-square test, and it may be easier to use `HWChisq` in these circumstances.

### Value

 `pval` p-value of the exact test `prob` probabilities of all possible samples with the same sample size and minor allele count `pofthesample` probability of the observed sample

### Author(s)

Jan Graffelman (jan.graffelman@upc.edu)

### References

Weir, B.S. (1996) Genetic data analysis II. Sinauer Associates, Massachusetts. See Chapter3.

Wigginton, J.E., Cutler, D.J. and Abecasis, G.R. (2005) A note on exact tests of Hardy-Weinberg equilibrium, American Journal of Human Genetics (76) pp. 887-893.

`HWLratio`, `HWChisq`

### Examples

```#
# Example autosomal marker
#
x <- c(298,489,213)
names(x) <- c("MM","MN","NN")
## Not run: HW.test <- HWExactPrevious(x,verbose=TRUE)
#