Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect

calculateSignificantLevel | Calculate significant level for hypo and hyper conserved... |

createDataStructure | Extract the number of conserved differentially methylated... |

createOutputDir | Create directories that will contained the results of the... |

demoForTransgenerationalAnalysis | The methylation information from samples over three... |

extractInfo | Extract the information specific to a subsection of the... |

formatInputMethylData | Permute dataset |

getGRangesFromMethylDiff | Transform results from a CpG site or region analysis done on... |

interGeneration | Calculate the intersection of the differentially methylated... |

isInterGenerationResults | Verify if a specific file containing intergenerational... |

loadAllRDSResults | Load all RDS files created by the permutation and observation... |

loadConvergenceData | Load convergence information from RDS files |

mergePermutationAndObservation | Merge the permutation results with the observation results. |

methylInheritanceAllResults | Print a 'methylInheritanceAllResults' object |

methylInheritance-package | methylInheritance: Permutation-Based Analysis associating... |

methylInheritanceResults | All observed and permutation results formatted in a... |

plotConvergenceGraph | Generate a graph showing the convergence for a permutation... |

plotGraph | Generate a graph for a permutation analysis |

readInterGenerationResults | Read and return intergenerational results contained in a RDS... |

runObservation | Run a differential methylation analysis on multi-generational... |

runOnePermutationOnAllGenerations | Run the analysis on one permutation dataset, including all... |

runPermutation | Run all permutations on the specified multi-generational... |

samplesForTransgenerationalAnalysis | All samples information, formated by 'methylKit', in a... |

saveInterGenerationResults | Save the result of on CpG site or tile analysis on all... |

validateExtractInfo | Validation of some parameters of the 'extractInfo' function |

validateLoadConvergenceData | Validation of some parameters of the 'loadConvergenceData'... |

validateMergePermutationAndObservation | Validation of some parameters of the... |

validateRunObservation | Validation of some parameters of the 'runObservation'... |

validateRunPermutation | Parameters validation for the 'runPermutation' function |

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