CLD.test {GeneGeneInteR} | R Documentation

## CLD (Composite Linkage Desequilibrium) based GGI analysis.

### Description

`CLD.test` performs a Gene-Gene Interaction (GGI) analysis based on the difference between the Composite Linkage Disequilibrium measured in cases and controls respectively.

### Usage

    CLD.test(Y, G1, G2, n.perm = 1000)

### Arguments

`Y` | numeric or factor vector with exactly two different values. `Y` is the response variable and should be of length equal to the number of rows of `G1` and `G2` arguments (number of individuals).
`G1` | SnpMatrix object. Must have a number of rows equal to the length of `Y`.
`G2` | SnpMatrix object. Must have a number of rows equal to the length of `Y`.
`n.perm` | positive integer. `n.perm` is the number of permutations performed to compute the pvalue. By default, `n.perm` is fixed to 1000.

### Details

The test statistic is based on Nagao normalized Quadratic Distance (NQD), as described in Rajapakse et al. (2012). The pvalue is calculated using `n.perm` permutations of `Y`.

### Value

A list with class `"htest"` containing the following components:

`statistic` | The value of the statistic CLD.
`p.value` | The p-value for the test.
`estimate` | The estimation of CLD
`parameter` | The number of permutations used to estimate the p-value.
`null.value` | The value of CLD under the null hypothesis.
`alternative` | a character string describing the alternative.
`method` | a character string indicating the method used.
`data.name` | a character string giving the names of the data.

### References

Indika Rajapakse, Michael D. Perlman, Paul J. Martin, John A. Hansen, and Charles Kooperberg. Multivariate detection of gene-gene interactions. Genetic Epidemiology, 36(6) :622-630, 2012.

### See Also

`GGI`

### Examples

    data(gene.pair)
    CLD.test(Y=gene.pair$Y, G1=gene.pair$G1,G2=gene.pair$G2)

[Package GeneGeneInteR version 1.6.0 Index]