MethylIT utility

bootstrap2x2 | bootstrap2x2 |

classPerform | Classification performance based on divergences of... |

colorBar | Color bar for heatmaps |

divTest | Group Comparisons of Information Divergences Based on... |

dmpDensity | Linear density of DMPs at a given genomic region |

evalDetection | Evaluate detection performance of a signal detector |

evaluateModel | Evaluate a model using the Akaike information criterion (AIC) |

findCutpoint | Find a cutoff of divergences of methylation level values |

gammaMixtCut | Cutpoint estimation based on Mixtures of Gamma Distributions |

GeneUpDownStream | Get Genes plus Up and Down Stream Regions |

getGRegionsStat2 | Statistic of Genomic Regions |

getGRegionsStat-methods | Statistic of Genomic Regions |

getMethContext | Get Methylation Context from a chromosome DNA sequence |

hclust_rect | Draw Rectangles with Background Colors Around Hierarchical... |

jensenSDiv | Compute Jensen-Shannon Divergence |

ksTest | Kolmogorov-Smirnov statistics |

predict.GammaMixt | Predict function for the DMP's Mixtures of Gamma... |

predict.ProbDistr | Predict function for probability distributions in Methyl-IT |

propTest | Beta Regression for methylation levels and rates |

rmstGR | Root Mean Square Test for Methylation Analysis |

shannonEntr | Compute Shannon Entropy |

signal2bins | Genomic Signal to Summarized Bins |

signals2bins | Genomic Signals to Summarized Bins |

simulateCounts | Simulate read counts of methylated and unmethylated cytosines |

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