pinnacle: Gene set enrichment analysis based on genomic intervals

correlationDecomp | Compute SVD of covariance matrix |

correlationSquaredDecomp | Compute SVD of squared correlation matrix |

dot-getScalingMatrixFromWeights | Projection on orthogal vector space |

dot-get_SigmaGamma | Extract scaling of random effects |

dot-projectionOntoExistingSpace | Projection on orthogal vector space |

dot-weight_fxn_internal | Scaled covariance between two peaks |

ESS | Compute effective sample size |

evalCorrelationDecomp | Evaluate SVD of correlation structure |

getCorrInGeneSet | Evaluate correlation of genes within each gene set |

getGeneMapping | Get mapping from differential analysis to genomic annotations |

getPeakGeneDistances | getPeakGeneDistances |

glsCovariance-class | Store covariance for glslr |

glsCovList-class | Store list of covariances for glslr |

glslr | Generalized least squares using precomputed eigen... |

glslrApply | Generalized least squares for many tests |

glslr-class | Generalized least squares low rank |

makeImageRect | Convert correlation matrix into triangle plot |

pinnacle | Evaluate gene set enrichments with Pinnacle |

pinnacleEnrich | Evaluate enrichment statistics |

plotCorrDistance | Plot correlation versus distance |

plotCorrTriangle | Plot triangle of correlation matrix |

plotDistanceWeights | Plot weights versus distance |

plotEnrichment | Plot enrichment results |

plotPinnacleResult | Plot panels of results |

print-glsCovariance | Print values |

print-glsCovList | Print values |

print-glslr | Print values |

print-spectralDecomp | Print values |

projectionLMM | Project response onto vector space |

setDecompRank | Truncate spectral decomposition |

setDecompRank-methods | Set the rank of a spectralDecomp object by truncation |

show-glsCovariance | Show values |

show-glsCovList | Show values |

show-glslr | Show values |

show-spectralDecomp | Show values |

spectralDecomp-class | Store results of SVD and eigen decomposition in standard... |

summary_glslr-class | Summary of glslr |

summary-glslr-method | Summarizing Generalized Linear Model Fits |

vcov-methods | Variance-covariance matrix |

weight_fxn | Scaled covariance between two peaks |

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