HWE {GeneticsBase} | R Documentation

## Test the significances of Hardy-Weinberg Equilibrium (dis)equilibrium) statistics

### Description

Test the significances of Hardy-Weinberg Equilibrium (dis)equilibrium) statistics for each marker in a data set.

### Usage

    HWE(object,
        test = c("exact", "permutation", "chisq"),
        B = 10000,
        R = 1000,
        correct = TRUE,
        conf = c(0.95),
        na.rm = TRUE,
        founderOnly = TRUE,
        ...)

### Arguments

`object` | a geneSet object.
`test` | specifys the test method. Available methods are “exact”, “permutation”, “chisq”.
`B` | an integer specifying the number of replicates used in the Monte Carlo test. Defaults to 10000.
`R` | Number of bootstrap iterations to use when computing the confidence interval. Defaults to 1000.
`correct` | see `diseq.ci`.
`conf` | Confidence level to use when computing the confidence level for linkage disequilibrium measures. Defaults to 0.95, should be in (0,1).
`na.rm` | logical. Should missing values be removed?
`founderOnly` | Indicates if only founders are used to do the test.
`...` | othere arguments used by the function `chisq.test`.

### Value

The function `HWE` returns a list:

`“diseq”` | a character string.
`call` | the matched call.
`“D”` | a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument `conf`. The first column is the estimated “D”. The next $p$ columns are estimated confidence limits for the confidence levels specified in the argument `conf`. The last two columns are the sample size and the p-value of the test that “D” is equal to zero.
`“D'”` | a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument `conf`. The first column is the estimated “D'”. The next $p$ columns are estimated confidence limits for the confidence levels specified in the argument `conf`. The last two columns are the sample size and the p-value of the test that “D'” is equal to zero.
`“r”` | a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument `conf`. The first column is the estimated “r”. The next $p$ columns are estimated confidence limits for the confidence levels specified in the argument `conf`. The last two columns are the sample size and the p-value of the test that “r” is equal to zero.
`“X$^2$”` | a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument `conf`. The first column is the test statistic “X$^2$” for HWE test. The next $p$ columns are zeros. The last two columns are the sample size and the p-value of the test for Hardy-Weinberg equilibrium.

### Author(s)

Gregory R. Warnes gregory.r.warnes@pfizer.com and Nitin Jain nitin.jain@pfizer.com

### Examples

    library(GeneticsBase)
    data(CAMP)

    HWE(CAMP)

[Package GeneticsBase version 1.2.0 Index]