CP/NNLS

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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]

References

^ Lawson, Daniel John; Hellenthal, Garrett; Myers, Simon; Falush, Daniel (January 2012). "Inference of population structure using dense haplotype data". PLOS Genetics. 8 (1): e1002453. doi:10.1371/journal.pgen.1002453. ISSN 1553-7404. PMC 3266881. PMID 22291602.
^ Lawson, Daniel. "ChromoPainter". people.maths.bris.ac.uk.
^ Järve, Mari; et al. (22 July 2019). "Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance". Current Biology. 29 (14): 2430–2441.e10. doi:10.1016/j.cub.2019.06.019. ISSN 0960-9822. PMID 31303491.
^ Saag, Lehti; et al. (3 July 2020). "Genetic ancestry changes in Stone to Bronze Age transition in the East European plain". Science Advances. 7 (4). bioRxiv 10.1101/2020.07.02.184507. doi:10.1126/sciadv.abd6535. PMC 7817100.

[1] Lawson, Daniel John; Hellenthal, Garrett; Myers, Simon; Falush, Daniel (January 2012). "Inference of population structure using dense haplotype data". PLOS Genetics. 8 (1): e1002453. doi:10.1371/journal.pgen.1002453. ISSN 1553-7404. PMC 3266881. PMID 22291602.

[2] Lawson, Daniel. "ChromoPainter". people.maths.bris.ac.uk.

[3] Järve, Mari; et al. (22 July 2019). "Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance". Current Biology. 29 (14): 2430–2441.e10. doi:10.1016/j.cub.2019.06.019. ISSN 0960-9822. PMID 31303491.

[4] Saag, Lehti; et al. (3 July 2020). "Genetic ancestry changes in Stone to Bronze Age transition in the East European plain". Science Advances. 7 (4). bioRxiv 10.1101/2020.07.02.184507. doi:10.1126/sciadv.abd6535. PMC 7817100.

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