cna | R Documentation |

Calculates the number of copy number aberrations

```
cna(
cnvData,
sample_column = 1,
segmentMean = (log(1.7, 2) - 1),
numProbes = NA,
segmentDistance = 0.2,
minSegSize = 10
)
```

`cnvData` |
dataframe containing following columns: Sample, Start, End, Num_Probes, Segment_Mean |

`sample_column` |
numerical value for the sample column number, default is 1 |

`segmentMean` |
numerical value for the minimum segment_mean cutoff/ threshold. Default is 0.2 |

`numProbes` |
Number of Probes |

`segmentDistance` |
Segment distance threshold |

`minSegSize` |
Minimum segment size |

Copy Number Aberrations (CNA) (Davidson JM, et al), are defined as a segment with copy number outside the pre-defined range of 1.7-2.3

`(\log_2 1.7 -1) \le \bar{y}_{S_i} \le (\log_2 2.3 -1)`

that is not contiguous with an adjacent independent CNA of identical copy number. For our purposes, we have adapted the range to be

`|\bar{y}_{S_i}| \ge |\log_2 1.7|`

, which is only slightly larger than the original.
It is nearly identical to countingBreakPoints, except this one calculates breaks as adjacent segments that have a difference in segment means of `\ge 0.2`

.

```
Total\ Copy\ Number\ Aberration = \sum^{R}_{i = 1} n_i \ where \
\bar{y}_{S_i}| \ge |\log_2{1.7}|, \
\bar{y}_{S_{i-1}} - \bar{y}_{S_i}| \ge 0.2, \
d_i \ge 10
```

Number of copy number aberrations between segments

`countingBreakPoints`

```
cna(cnvData = maskCNV_BRCA)
```

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