canopy.cluster {Canopy} | R Documentation |

## EM algorithm for multivariate clustering of SNAs

### Description

EM algorithm for multivariate clustering of SNAs.

### Usage

```
canopy.cluster(R, X, num_cluster, num_run, Mu.init = NULL, Tau_Kplus1 = NULL)
```

### Arguments

`R` |
alternative allele read depth matrix |

`X` |
total read depth matrix |

`num_cluster` |
number of mutation clusters (BIC as model selection metric) |

`num_run` |
number of EM runs for estimation for each specific number of clusters (to avoid EM being stuck in local optima) |

`Mu.init` |
(optional) initial value of the VAF centroid for each mutation cluster in each sample |

`Tau_Kplus1` |
(optional) pre-specified proportion of noise component in clustering, uniformly distributed between 0 and 1 |

### Value

Matrix of posterior probability of cluster assignment for each mutation.

### Author(s)

Yuchao Jiang yuchaoj@wharton.upenn.edu

### Examples

```
data(AML43)
R = AML43$R
X = AML43$X
Mu = AML43$Mu
Tau = AML43$Tau
pG = canopy.cluster.Estep(Tau, Mu, R, X)
```

[Package

*Canopy*version 1.3.0 Index]