## CNA-seq / Normalize copy number data

### Description

Normalizes copy number data before segmentation.

### Parameters

- Normalization method (median, mode, none) [median]
- Smooth outliers (yes, no) [yes]

### Details

Copy number data is normalized using the chosen method. Optionally, outliers can be smoothed using using the DNAcopy package.

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

### Output

Normalized values.

### References

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