aCGH / Call copy number aberrations

Description

Call copy number aberrations from aCGH log ratios.

Parameters

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.

A plot is also returned that shows the frequencies of gains (blue) and losses (red).

References

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