Copy number aberrations / Normalize copy number data

Description

Normalizes copy number data before segmentation.

Parameters

• Normalization method (median, mode, none) [median]
• Smooth outliers (yes, no) [yes]
• Number of chromosomes (...) [23]

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