Description Usage Arguments Value Examples

the MGN distribution model the joint distribution, pi(lambda,delta), by a K-component MGN distribution, and allows degenerate normal for delta when the null hypothesis is simple.

1 |

`data` |
the RNA-seq data, should be the output from RNASeq.Data |

`nK` |
the number of components in MGN. When testing for fold-changes (FC), nK includes all components, when testing for differential expression (DE), nK only includes the components that are NOT degenerated. |

`p0` |
the proportion of null genes when testing for DE genes. |

`d0` |
the point where 'delta' is degerated, default is 0 when testing for DE genes. |

`nK0` |
the number of components that are degenerated when testing for DE genes. |

`iter.max` |
maximium number of interations in the EM algorithm |

`print.steps` |
print the esimates of MGN in each iteration step, if TRUE. Default is FALSE |

`MGN0` |
The initialization of the MGN. It should be a data.frame with 5 columns: pr, alpha, beta, mu, sigma. The methods of moment estimation will be used if not provided. |

`model` |
data model, can be 'nbinom' or 'poisson'. the default will be the same as in 'data' |

`nMC` |
the number of random samples from Gamma and Normal distrubitons in the Monte-Carlo simulation. |

`MGN` |
The estimated MGN distribution, as a data.frame with 5 columns: pr, alpha,beta,mu,sigma. pr: the proportion (weight) of each component \ alpha: alpha in the Gamma distribution \ beta: beta in the Gamma distribution \ mu: mu (mean) of the Normal distribution\ sigma: sigma (standard deviation) of the Normal distribution. sigma=0 is allowed for degenerated Normal |

`lam` |
the shrinked estimation of lambda (mean expression for each gene) |

`del` |
the shrinked estimation of delta (log-fold change) for each gene |

1 | ```
#### see examples by typing 'help(test.AMAP)'
``` |

AMAP.Seq documentation built on May 29, 2017, 8:23 p.m.

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