Description Usage Arguments Details Value References See Also Examples

`CLD.test`

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

1 | ```
CLD.test(Y, G1, G2, n.perm = 1000)
``` |

`Y` |
numeric or factor vector with exactly two different values. |

`G1` |
SnpMatrix object.
Must have a number of rows equal to the length of |

`G2` |
SnpMatrix object.
Must have a number of rows equal to the length of |

`n.perm` |
positive integer. |

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`

.

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. |

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.

1 2 |

GeneGeneInteR documentation built on May 2, 2018, 4:26 a.m.

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