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. The optional smoothing over a specified number of bins is implemented in the QDNAseq package. 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
Scheinin et al. (2014) DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res In Press.
Wiel et al. (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23: 892-894