CNA-seq / Segment copy number data

Description

Segments copy number data.

Parameters

• Minimum number of features per segment (2, 3, 4, 5) [2]
• Minimum number of SDs between segments [0.0]
• Significance level (...) [1E-10]
• Number of bins to smooth signal over (...) [1]
• Re-normalize (yes, no) [yes]

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 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.

Output

The inputted log ratios are accompanied with segmented log ratios.

References

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

QDNAseq:
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.

CGHcall:
Wiel et al. (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23: 892-894