countingBaseSegments | R Documentation |

Function for counting altered base segments

```
countingBaseSegments(
cnvData,
sample_column = 1,
segmentMean = 0.2,
numProbes = NA
)
```

`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 |

The Altered Base Segment calculation takes all the CNV data for a single patient and first filters it for a segmentation mean of > 0.2 and, if specified, the minimum number of probes covering that area. Then, it calculates the sums of the lengths of each segment for a particular patient and outputs that.

```
Number\ of\ Altered\ Bases = \sum^{R}_{i = 1} d_i\ where\ |\bar{y}_{S_i}| \ge 0.2
```

Number of Base segments for each unique sample

```
countingBaseSegments(cnvData = maskCNV_BRCA)
```

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