mstep {ebGenotyping} | R Documentation |

This function calculates the CM steps of ECM algorithm for the model described in 'An Empirical Bayes Method for Genotyping and SNP detection Using Multi-sample Next-generation Sequencing Data'.

```
mstep(mu0, delta0, zm1, z0, zp1, dat, cvg, eps = 1e-06)
```

`mu0` |
a vetor of the same length as number of positions: the initial value of position effect mu. |

`delta0` |
a vetor of the same length as number of samples: the initial value of sample effect delta. |

`zm1` |
the output of estep: the posterior probabilities of genotype RR for n samples at m positions |

`z0` |
the output of estep: the posterior probabilities of genotype RV for n samples at m positions |

`zp1` |
the output of estep: the posterior probabilities of genotype VV for n samples at m positions |

`dat` |
a n*m matrix: the ith row, jth column of the matrix represents the non-reference counts of ith sample at jth position. |

`cvg` |
a n*m matrix: the ith row, jth column of the matrix represents the depth of ith sample at jth position. |

`eps` |
a single value: a threshold to control the convergence criterion. The default is 1e-06. |

The value of mu and delta must satisfy that each element of outer(delta,mu,"+") must less than zero. This is the requirement of the model described in 'An Empirical Bayes Method for Genotyping and SNP detection Using Multi-sample Next-generation Sequencing Data'.

`mu` |
the optimal value of mu in current CM steps |

`delta` |
the optimal value of delta in current CM steps |

`pRR` |
the optimal value of the probability of RR in current CM steps |

`pRV` |
the optimal value of the probability of RV in current CM steps |

The most important function in this package is "ecm". "mstep" is a function called by "ecm" to realize one M step(several CM steps) in the whole process of iteration in "ecm".

Na You <youn@mail.sysu.edu.cn> and Gongyi Huang<53hgy@163.com>

Na You and Gongyi Huang.(2016) An Empirical Bayes Method for Genotyping and SNP detection Using Multi-sample Next-generation Sequencing Data.

[Package *ebGenotyping* version 2.0.1 Index]