Description Usage Arguments Details Value Author(s) References See Also

Determines the importance of interactions found by `logic.bagging`

or `logicFS`

by an Empirical Bayes Analysis of Microarrays (EBAM). Only available for the classification
and the logistic regression approach of logic regression.

1 |

`object` |
either an object of class |

`data` |
a data frame or matrix consisting of 0's and 1's in which each column corresponds
to one of the explanatory variables used in the original analysis with |

`cl` |
a numeric vector of 0's and 1's specifying the class labels of the observations in |

`storeEBAM` |
logical specifying whether the output of the EBAM analysis should be stored in the
output of |

`...` |
further arguments of |

For each interaction found by `logic.bagging`

or `logicFS`

, the posterior probability
that this interaction is significant is computed using the Empirical Bayes Analysis of Microarrays (EBAM).
These posterior probabilities are used as the EBAM based importances of the interactions.

The test statistic underlying this EBAM analysis is Pearson's ChiSquare statistic. Currently, the value of this statistic is computed without continuity correction.

Contrary to `vim.logicFS`

(and `vim.norm`

and `vim.signperm`

),
`vim.ebam`

does neither take the logic regression models into acount nor uses the out-of-bag
observations for computing the importances of the identified interactions. It "just" tests each
of the found interactions on the whole data set by calculating Pearson's ChiSquare statistic for
each of these interactions and performing an EBAM analysis. It is, therefore, highly recommended
to use an independent data set for specifying the importances of these interactions with `vim.ebam`

.

An object of class `logicFS`

containing

`primes` |
the prime implicants, |

`vim` |
the posterior probabilities of the interactions, |

`prop` |
NULL, |

`type` |
NULL, |

`param` |
further parameters (if |

`mat.imp` |
NULL, |

`measure` |
"EBAM Based", |

`threshold` |
the value of |

`mu` |
NULL, |

`ebam` |
an object of class |

Holger Schwender, holger.schwender@hhu.de

Schwender, H. and Ickstadt, K. (2008). Empirical Bayes Analysis of
Single Nucleotide Polymorphisms. *BMC Bioinformatics*, 9:144.

`logic.bagging`

, `logicFS`

,
`vim.logicFS`

, `vim.norm`

, `vim.chisq`

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