In each iteration, the algorithm iteratively updates each entry in the binary matrix Z, loading matrix W and factor activity matrix X, as well as other model parameters.

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`matrixY` |
The input treatment response matrix. It has dimension G by J,where G is the number of probesets and J is the number of different treatments. The (g,j)-th entry represents the ratio of the expression of the g-th probeset after and before the j-th treatment. |

`matrixL` |
The binary probeset-pathway association matrix.It has dimension G by K. If the (g,k)-th entry has value 1, it indicates that the g-th probeset is involved in the k-th pathway; and the (g,k)-th entry takes value 0 if there is no association relationship. |

`eta0` |
The bernoulli probability of entries in matrix Z taking a non-zero value given that the corresponding entry in matrix L is zero |

`eta1` |
The bernoulli probability of entries in matrix Z taking the value zero given that the corresponding entry in matrix L is one |

`alpha_tau` |
The alpha parameter of Gamma distribution used for the simulation of noise, default value=1 |

`beta_tau` |
The beta parameter of Gamma distribution used for the simulation of noise, default value=0.01 |

`tau_sig` |
Pre-defined precision of each entry in the factor loadings matrixW, default value=0 |

`max_iter` |
The number of iterations of the collaped Gibbs sampling algorithm, default=10000 |

`thin` |
The number of iteration cycle for the record of Gibbs samples. For the convenience of storage, the result of the Gibbs sampling will be kept every other "thin" iterations to alliviate the auto-correlation problem between adjacent interations of the Gibbs sampling process |

`alpha_sigma` |
the alpha parameter for the Gamma prior for matrixW |

`beta_sigma` |
The beta parameter for the Gamma prior for matrixW |

`file_name` |
name of the file saving the result |

The algorithm will store the inferred binary indicator matrix Z, loading matrix W and factor activity matrix X (as well as tau_g if not pre-difined) in each thinned iteration and write them into .RData file with name defined by the user.

Haisu Ma<haisu.ma@yale.edu>

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Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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