Matrix Based Analysis for State-space Inference and Clustering.

averageMGC | Compute the average mappability and GC scores over a set of... |

bkng_mean | Compute the background means. |

ChIPInputMatch | Match the ChIP files with input files. |

generateReadMatrices | Map the reads for each pair of matched ChIP and input files... |

generateSyntheticData | Generate synthetic BED data, M and GC files. |

MBASIC | Bayesian clustering model for a state-space matrix. |

MBASIC.binary | Bayesian clustering model for binary state matrix with prior... |

MBASIC.binary.all | Bayesian clustering model for binary state matrix with prior... |

MBASICFit-class | An S-4 class containing the model fit information for MBASIC... |

MBASIC.full | Simultaneously fitting MBASIC model for different numbers of... |

MBASIC.MADBayes | MAD-Bayes method to fit the MBASIC model. |

MBASIC.MADBayes.full | MAD-Bayes method to fit the MBASIC model. |

MBASIC.pipeline | The pipeline for fitting a MBASIC model for sequencing data. |

MBASIC.sim | Simulate data for the general MBASIC model. |

MBASIC.sim.binary | Simulate data for the MBASIC model with binary states. |

MBASIC.sim.state | Simulate the state matrix for general MBASIC models. |

MBASIC.state | Bayesian clustering model for a state-space matrix. |

plot-methods | Plot the state probability for a fitted MBASIC model. |

readReads | Read sequencing reads from either a BAM or a BED file. |

write.out | Write the message to an output file. |

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