Description Usage Arguments Value Author(s) Examples

View source: R/canopy.cluster.R

EM algorithm for multivariate clustering of SNAs.

1 | ```
canopy.cluster(R, X, num_cluster, num_run, Mu.init = NULL, Tau_Kplus1 = NULL)
``` |

`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 |

Matrix of posterior probability of cluster assignment for each mutation.

Yuchao Jiang [email protected]

1 2 3 4 5 6 |

```
Loading required package: ape
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
Loading required package: pheatmap
Loading required package: scatterplot3d
```

Canopy documentation built on Dec. 23, 2017, 5:09 p.m.

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