Model-based gene set analysis

alphaMcmcPost-methods | posterior estimates of the parameter alpha for each MCMC run |

alphaPost-methods | Posterior for alpha |

betaMcmcPost-methods | posterior estimates of the parameter beta for each MCMC run |

betaPost-methods | Posterior for beta |

createMgsaGoSets | This functions takes a 1:1 mapping of go.ids to items and... |

example-go | Example GO sets for mgsa |

example-o | Example objects for mgsa |

itemAnnotations-methods | Item annotations of a MgsaSets |

itemIndices-methods | Item indices of a MgsaSets |

length-methods | Length of a MgsaSets. |

MgsaGoSets-class | Gene Ontology annotations |

MgsaMcmcResults-class | Instances of this class are used to hold the additional... |

mgsa-methods | Performs an MGSA analysis |

mgsa-package | Model-based gene set analysis |

MgsaResults-class | Results of an MGSA analysis |

MgsaSets-class | Sets of items and their annotations |

nsamples-methods | How many samples per MCMC run collected |

plot-MgsaResults-method | Plot method for MgsaResults objects |

pMcmcPost-methods | posterior estimates of the parameter p for each MCMC run |

populationSize-methods | Size of the population of a MgsaResults |

pPost-methods | Posterior for beta |

readGAF | Read a Gene Ontology annotation file |

restarts-methods | How many MCMC runs |

setAnnotations-methods | Set annotations of a MgsaSets |

setsMcmcPost-methods | posterior estimates of the the set marginal probabilities for... |

setsResults-methods | Posterior for each set |

show-MgsaResults-method | Show an MgsaResults |

show-MgsaSets-method | Show an MgsaSets |

steps-methods | How many steps per MCMC run |

studySetSizeInPopulation-methods | Size of the study set of a MgsaResults |

subMgsaSets-methods | Subset of an MgsaSets |

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