Description Usage Arguments Value Examples

Find top Gene Ontology terms for given genes.

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`groups` |
a MultiAssayExperiment object containing an ExperimentList class object representing gene expressions for at least 3 cohorts. Rows must be named with genes' aliases. The order of samples and genes has to be the same for each ExperimentList class object. |

`topAOV` |
A numeric value, a number of most significantly differentiated genes to be returned. |

`sig.levelAOV` |
a numeric value, a significance level
used in BH correction for multiple testing ( |

`parallel` |
A logical value indicating if a task should be run on more than one core. |

`grouped` |
A method of grouping genes, one of 'tukey' and 'clustering'. |

`sig.levelGO` |
A numeric value, a significance level used
in BH correction for multiple testing ( |

`minGO` |
A minimum number of functions that a gene needs to represent to be considered as frequent. |

`maxGO` |
A maximum number of functions that a gene needs to represent to be considered as frequent. |

`clust.metric` |
The method to calculate a distance measure used in hierarchical clustering, possible names: "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". |

`clust.method` |
The agglomeration method used to cluster genes. This should be #'one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). |

`dist.matrix` |
A matrix with calculated distances to be
used as a metric by |

`topGO` |
A number of the most characteristic functions of groups of genes to be returned. |

`sig.levelTUK` |
A numeric value, a significance level used in
Tukey's all pairwise comparison ( |

`onto` |
An ontology or ontologies to be searched for significant GO terms, at least one of 'MF' (molecular function), 'BP' (biological process), and 'CC' (cellular component). |

`extend` |
A logical value indicating if an extended version of the output should be presented. |

`over.rep` |
A logical value indicating if an over represented GO terms should be presented in the plot. |

A data frame containing the top gene ontology terms for each group of genes and the gene aliases.

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