Coordinate Covariation Analysis

aggregateSignal | Score a region set using feature contribution scores |

aggregateSignalGRList | Score many region sets |

atf3_chr1 | Atf3 binding regions. |

brcaATACCoord1 | A GRanges object with coordinates for select BRCA ATAC-seq... |

brcaATACData1 | A matrix with ATAC-seq counts in select peak regions from... |

brcaMCoord1 | A GRanges object with genomic coordinates for cytosines from... |

brcaMetadata | A data.frame with patient metadata for breast cancer... |

brcaMethylData1 | A matrix with DNA methylation levels from some CpGs on... |

brcaPCScores | A matrix with principal component scores for PCs 1-4 for four... |

brcaPCScores657 | A data.frame with principal component scores for PCs 1-4 for... |

COCOA | Coordinate Covariation Analysis (COCOA) |

convertToFromNullDist | Converts COCOA permutation results to null distributions and... |

esr1_chr1 | Estrogen receptor alpha binding regions. |

gata3_chr1 | Gata3 binding regions. |

getGammaPVal | Get a p-value for region set scores based on a gamma... |

getMetaRegionProfile | Create a "meta-region" profile |

getPermStat | Get p-value or z-score based on permutation results |

getTopRegions | Get regions that are most associated with target variable |

nrf1_chr1 | Nrf1 binding regions. |

plotAnnoScoreDist | Plot ranked region set scores, annotating groups of interest |

regionQuantileByTargetVar | Visualize how individual regions are associated with target... |

rsRankingIndex | Get indices for top scored region sets |

rsScoreHeatmap | Heatmap of region set scores |

rsScores | Example COCOA Results (made up) |

runCOCOA | Run COCOA: quantify inter-sample variation, score region sets |

runCOCOAPerm | Run COCOA permutations to get p-values |

signalAlongAxis | Visualize how genomic signal in a region set changes along a... |

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