Description Usage Arguments Details Value References See Also Examples

`KCCA.test`

performs a Gene-Gene Interaction (GGI) analysis based on the
difference of canonical correlations between cases and controls. The "kernel trick" is applied to the canonical correlation to allow the detection of non-linear co-association.

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`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 |

`kernel` |
A character string matching one of the kernel name in : "rbfdot","polydot","tanhdot","vanilladot","laplacedot","besseldot","anovadot","splinedot". For more details regarding kernel function see |

`n.boot` |
positive integer. |

`sigma` |
The inverse kernel width used by the Gaussian the Laplacian ( |

`degree` |
The degree of the polynomial ( |

`scale` |
The scaling parameter of the polynomial ( |

`offset` |
The offset used in a polynomial ( |

`order` |
The order of the Bessel function to be used as a kernel ( |

The test statistic is based on the difference between a Fisher's transformation of the maximum of the kernelized canonical correlations in cases and controls. To calculate the test statistic for the interaction pvalue, `KCCA.test`

estimates the variance of the Fisher's transformation of the maximum of the kernelized canonical correlations in cases and controls using a bootstrap method. The computation of `kcca.`

can be very long.

A list with class `"htest"`

containing the following components:

`statistic` |
The value of the statistic KCCU. |

`p.value` |
The p-value for the test. |

`estimate` |
A vector of the Fisher's transformed maximum kernel canonical correlation coefficient in cases and controls. |

`parameter` |
The number of boostrap samples used to estimate the p-value. |

`null.value` |
The value of KCCU 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. |

Yuan, Z. et al. (2012): Detection for gene-gene co-association via kernel canonical correlation analysis, BMC Genetics, 13, 83.

Larson, N. B. et al. (2013): A kernel regression approach to gene-gene interaction detection for case-control studies, Genetic Epidemiology, 37, 695-703.

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MathieuEmily/GeneGeneInteR documentation built on Jan. 13, 2018, 6:55 a.m.

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