CP/NNLS explained

CP/NNLS, standing for "ChromoPainter (CP) non-negative least squares (NNLS)" is a statistical method used in genetics. "ChromoPainter" is the name of a tool for finding haplotypes in sequence data, in which each individual is "painted" as a combination of all other sequences. It is used in Principal Components Analysis (PCA) to create data summaries, or dating admixture events.^{[1] [2]} Non-negative least squares (NNLS) is a kind of regression analysis, which aims at finding the best possible correlation between a large set of dependent variables. It here used within the functionalities of ChromoPainter.

CP/NNLS is often used in conjunction with qpAdm.^{[3] [4]}

Notes and References

1. Lawson . Daniel John . Hellenthal . Garrett . Myers . Simon . Falush . Daniel . Inference of population structure using dense haplotype data . PLOS Genetics . January 2012 . 8 . 1 . e1002453 . 10.1371/journal.pgen.1002453 . 22291602 . 3266881 . 1553-7404 . free .
2. Web site: Lawson . Daniel . ChromoPainter . people.maths.bris.ac.uk.
3. Järve . Mari . Saag . Lehti . Scheib . Christiana Lyn . Pathak . Ajai K. . Montinaro . Francesco . Pagani . Luca . Flores . Rodrigo . Guellil . Meriam . Saag . Lauri . Tambets . Kristiina . Kushniarevich . Alena . Solnik . Anu . Varul . Liivi . Zadnikov . Stanislav . Petrauskas . Oleg . Avramenko . Maryana . Magomedov . Boris . Didenko . Serghii . Toshev . Gennadi . Bruyako . Igor . Grechko . Denys . Okatenko . Vitalii . Gorbenko . Kyrylo . Smyrnov . Oleksandr . Heiko . Anatolii . Reida . Roman . Sapiehin . Serheii . Sirotin . Sergey . Tairov . Aleksandr . Beisenov . Arman . Starodubtsev . Maksim . Vasilev . Vitali . Nechvaloda . Alexei . Atabiev . Biyaslan . Litvinov . Sergey . Ekomasova . Natalia . Dzhaubermezov . Murat . Voroniatov . Sergey . Utevska . Olga . Shramko . Irina . Khusnutdinova . Elza . Metspalu . Mait . Savelev . Nikita . Kriiska . Aivar . Kivisild . Toomas . Villems . Richard . 1. Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance . Current Biology . 22 July 2019 . 29 . 14 . 2430–2441.e10 . 10.1016/j.cub.2019.06.019 . 31303491 . 0960-9822. free .
4. Saag . Lehti . Vasilyev . Sergey V. . Varul . Liivi . Kosorukova . Natalia V. . Gerasimov . Dmitri V. . Oshibkina . Svetlana V. . Griffith . Samuel J. . Solnik . Anu . Saag . Lauri . D’Atanasio . Eugenia . Metspalu . Ene . Reidla . Maere . Rootsi . Siiri . Kivisild . Toomas . Scheib . Christiana Lyn . Tambets . Kristiina . Kriiska . Aivar . Metspalu . Mait . 1. Genetic ancestry changes in Stone to Bronze Age transition in the East European plain . 3 July 2020 . 10.1126/sciadv.abd6535. 10.1101/2020.07.02.184507 . Science Advances. 7 . 4 . 7817100 .