Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

assocPvalBySetPlot | Create a Density Plot of P-Values, Highlighting SNPs Within a... |

createArrayData | Create a GRanges Object for a GWAS data.frame |

degreesOfFreedom-method | ~~ Methods for Function 'degreesOfFreedom' ~~ |

exampleArrayData | SNP Array Data to Use for Gene Set Analysis |

geneSetAnalysis | Data to run gene set analysis methods |

geneSetName-methods | ~~ Methods for Function 'geneSetName' ~~ |

GeneSetResult-class | Class '"GeneSetResult"' |

GeneSetResultCollection-class | Class '"GeneSetResultCollection"' |

geneSets | Gene Set Collection object |

geneToSNPList | Translate a List of Gene Ids to Their Corresponding SNP Ids |

glossi | Calculate a Chi-squared Statistic and P-Value for Independent... |

glossiMarginal | Calculate a Chi-squared Statistic and P-Value for Items in a... |

GLOSSIResult-class | Class '"GLOSSIResult"' |

GLOSSIResultCollection-class | Class '"GLOSSIResultCollection"' |

plotPvals | Create a Plot of P-Values Against Number of SNPs per Set for... |

pValue-method | ~~ Methods for Function 'pValue' ~~ |

show-methods | ~~ Methods for Function 'show' in Package 'base' ~~ |

simulate_chisq | Simulate a Chi-squared Statistic from a Distribution with a... |

simulatedStats-method | ~~ Methods for Function 'simulatedStats' ~~ |

statistic-methods | ~~ Methods for Function 'statistic' ~~ |

vegas | Calculate the P-Value for a Set Using the VEGAS Method |

vegasMarginal | Calculate the P-Value for a Set Using the VEGAS Method |

VEGASResult-class | Class '"VEGASResult"' |

VEGASResultCollection-class | Class '"VEGASResultCollection"' |

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