## Copy number aberrations / Segment copy number data

### Description

Segments copy number data (either aCGH log ratios or log2-transformed NGS data).

### Parameters

- Normalization method (median, mode, none) [none]
- Number of chromosomes (...) [23]
- Minimum number of probes per segment (2, 3, 4, 5) [2]
- Minimum number of SDs between segments [0.0]

### Details

Log ratios are segmented using DNAcopy. Segments are consecutive areas that most likely share the same copy number and are separated by breakpoints.

The input data must contain these columns: chromosome, start, end.

### Output

The inputted log ratios are accompanied with segmented log ratios.

### References

DNAcopy:
Venkatraman et al. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663