Description Usage Arguments Value Examples

Starting from a matrix of coverages, the corresponding matrix of copy numbers is calculated. The caluculation includes a sample normalization step and a amplicon normalization step.

1 | ```
calculate.CN(coverage, scale.amplicon=NULL)
``` |

`coverage` |
A numeric matrix containing the coverages of each amplicon (rows) in each sample (columns). |

`scale.amplicon` |
Method for amplicon normalization. If |

Matrix of copy numbers with the amplicon scaling factors (`"scale.amplicon"`

) as attribute.

1 2 3 4 5 | ```
## Not run:
data(coverage)
CN <- calculate.CN(coverage)
## End(Not run)
``` |

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