Segments copy number data.
Log ratios are segmented using DNAcopy. Segments are consecutive areas that most likely share the same copy number and are separated by breakpoints. Optionally, a re-normalization can be performed with CGHcall. This recursively searches for the interval containing the most segmented data, decreasing the interval length in each recursion. The recursive search makes the post-segmentation normalization robust against local maxima. This function is particularly useful for profiles for which, after segmentation, the 0-level does not coincide with many segments. It is more or less harmless to other profiles.
The input data must contain these columns: chromosome, start, end.
The inputted log ratios are accompanied with segmented log ratios.
Venkatraman et al. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663
Wiel et al. (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23: 892-894