Call copy number aberrations from aCGH log ratios.
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.
The inputted log ratios are accompanied with segmented log ratios.
A plot is also returned that shows the frequencies of gains (blue) and losses (red).
DNAcopy:
Venkatraman et al. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663