Description Usage Arguments Value Examples

Starting from a matrix of coverages, the corresponding matrix of copy numbers is calculated. A null model for significance assessment of copy number alterations is fitted. Each amplicon in each sample is assessed for significance. Summarized copy numbers and p-values for genes are calculated as descibed below.

1 | ```
assess.CNA(coverage.target, coverage.source=NULL, method.pooled="amplicon", thres.cov=100)
``` |

`coverage.target` |
A numeric matrix containing the target coverages of each amplicon (rows) in each sample (columns). The target data are investigated for copy number alterations. |

`coverage.source` |
A numeric matrix containing the source coverages of each amplicon (rows) in each sample (columns).
The source data are used to fit a null model. If |

`method.pooled` |
Method used for the estimation of the null model. Either one common null model for all amplicons
( |

`thres.cov` |
Theshold for the minimal mean coverage of an amplicon to be included in the analysis. |

List containing the following elements: Matrix of copy numbers with the estimated null model (`"model"`

), estimates of copy numbers (`"CN.a"`

and `"CN.g"`

) for amplicons and genes as well as p-values of copy number alterations (`"P.a"`

and `"P.g"`

) for amplicons and genes. Copy numbers for genes are calculated as average of the copy numbers of all amplicons interrogating the gene, p-values for genes are calculated using Fisher's method.

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

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