Perform methylation analysis

analysisRegionResults | Old class to encapsulate results (deprecated in new version) |

analysisResults | Old class to encapsulate results (deprecated in new version) |

calculateRelevantSNPs | Calculate the SNPs correlated to cpgs |

computeRDAR2 | Compute signification of RDA test |

correlationMethExprs | Computes the correlation between methylation and expression |

correlationMethSNPs | Computes the correlation between methylation and SNPs |

createRanges | Create 'GenomicRanges' from data.frame |

DAPipeline | Perform differential methylation analysis |

DAProbe | Perform per probe analysis |

DARegion | Detect regions differentially methylated |

DARegionAnalysis | Analyse methylation or expression in a specific range |

explainedVariance | Calculate R2 for different variables |

exportResults | Exports results data.frames to csv files. |

filterResults | Filter the data.frame obtained from probe analysis |

filterSet | Filter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet' |

getGeneVals | Get all probes related to a gene |

getProbeResults | Obtain probe results from a 'ResultSet' |

getRDAresults | Get a summary of RDA results |

MEAL | MEAL (Methylation and Expression AnaLizer): Package for... |

MEAL-defunct | Defunct functions |

normalSNP | Normalize SNPs values |

plotBestFeatures | Plot best n cpgs |

plotFeature | Plot values of a feature |

plotLM | Plot a vector of R2 |

plotRDA | Plot RDA results |

plotRegion | Plot results in a genomic region |

prepareMethylationSet | Generating a 'MethylationSet' |

preparePhenotype | Process a table of phenotypes |

RDAset | Calculate RDA for a set |

runBlockFinder | Run blockFinder |

runBumphunter | Run bumphunter |

runDiffMeanAnalysis | Run differential mean analysis |

runDiffVarAnalysis | Run differential variance analysis |

runDMRcate | Run DMRcate |

runPipeline | Perform differential methylation analysis |

runRDA | Calculate RDA for a set |

runRegionAnalysis | Run different DMR detection methods |

topRDAhits | Get the top features associated with the RDA |

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