Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection

betaParametrizationConverters | Functions to convert between shape parameters a and b for... |

estimateMAF1s | Function that given observed count data returns a maximum... |

estimateMAF2s | Function that given observed count data returns a maximum... |

FreemanTukeyFunctions | Freeman-Tukey transformation functions. |

generatingBetaBinomialCounts | Functions to generate beta-binomial random variables. |

getPFinal | Function that adjusts true underlying allele frequency for... |

getSimulationPvalue | Function to calculate simulations-based p-values |

logLikelihoodCalculator1s | Function that given observed count data along a known... |

logLikelihoodCalculator2s | Function that given observed count data along a known... |

maxLogLikelihoodCalculator1s | Function that given observed count data along a known... |

maxLogLikelihoodCalculator2s | Function that given observed count data along a known... |

MBASED | MBASED |

MBASEDMetaAnalysis | Generic function to perform standard meta analysis. |

MBASEDMetaAnalysisGetMeansAndSEs | Helper function to obtain estimate of underlying mean and the... |

MBASEDVectorizedMetaprop | Vectorized wrapper around metaprop() function from R package... |

MBASEDVectorizedPropDiffTest | Vectorized wrapper around a test for difference of 2... |

runMBASED | Main function that implements MBASED. |

runMBASED1s | Function that runs single-sample ASE calling using data from... |

runMBASED1s1aseID | Function that runs single-sample ASE calling using data from... |

runMBASED2s | Function that runs between-sample (differential) ASE calling... |

runMBASED2s1aseID | Function that runs between-sample (differential) ASE calling... |

shiftAndAttenuateProportions | Helper function to adjust proportions for pre-existing... |

testNumericDiff | Function that checks to see if the difference between 2... |

testQuantiles | Function to test quantile equality for theoretical and... |

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