EstimateClonality is an R package which uses read count and copy number information to temporally and clonally dissect SNVs, written by Nicholas McGranahan ([email protected]).
This version fixes some issues in the original code and makes a little optimization.
- add some annotations.
- add GD annotations.
For the genome doubling (function genome.doub.sig), the NULL hypothesis is that the evolution of high-ploidy results from a process of successive partial amplifications (independent amplifications between chromosomal arms) and the alternative hypothesis is that the evolution of tumor karyotypes results from whole-genome doubling (doubling all chromosomal at a time).
References:
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Dewhurst, S. M., McGranahan, N., Burrell, R. A., Rowan, A. J., Gronroos, E., Endesfelder, D., . . . Swanton, C. (2014). Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov, 4(2), 175-185. doi:10.1158/2159-8290.CD-13-0285
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Carter, S. L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T., . . . Getz, G. (2012). Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol, 30(5), 413-421. doi:10.1038/nbt.2203
- The original R package is not compatible with sequenza version 3.0. Now the earlyORlate() function is compatible.
- Added support for FACETS and CNVKIT (non ASCAT data).
- Part of the code is simplified.