Description Arguments Author(s)

parameters name and their descriptions

`methReads` |
The matrix |

`totalReads` |
The matrix |

`methLevels` |
The matrix |

`rowRanges` |
A |

`colData` |
Object of class |

`metadata` |
A |

`object` |
A |

`value` |
An integer matrix |

`name` |
A character list |

`obj1` |
A |

`obj2` |
A |

`files` |
A character list |

`file` |
A character |

`nCores` |
An integer value specifying the number of machine cores for parallel computing |

`mc.cores` |
An integer greater than 0 |

`pSize` |
An integer value specifying the number of cytosines in a regrion to be used in a Bayesian functiona regression model for DMC detection |

`bwa` |
An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the group-specific effects of the Bayesian functional regression model |

`bwb` |
An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the individual-specific effects of the Bayesian functional regression model |

`nBurn` |
An integer value specifying the number of burn-in samples |

`nThin` |
An integer value specifying the thining number in MCMC |

`nMC` |
An integer value specifying the number of MCMC samples after burn-in |

`sdv` |
An double value specifying the standard deviation of priors |

`alpha` |
A numeric value specifying the level of |

`col` |
A character vector indicating which colors to alternate. |

`sfiles` |
A logical value indicating whether files to be saved or not. |

`region` |
An integer vector of length two specifying which subset of the object to be plotted |

`nSplit` |
A integer value specifying the number of subsets must be done for plotting the results of DMC identification |

`parList` |
A list specifying plots parameters, see |

`...` |
other possible parameters |

Farhad Shokoohi <shokoohi@icloud.com>

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