Abstract
Using data from a case-control study on schizophrenia, we demonstrate the use of PLS regression in constructing predictors of a phenotype from Single Nucleotide Polymorphisms (SNPs). We consider straightforward application of PLS regression as well as two hybrid methods, in which PLS regression scores are used as input for a tree-growing algorithm and a clustering algorithm respectively. We compare these approaches with other classic predictors used in statistical learning, showing that our PLS-based hybrid methods outperform both classic predictors and straightforward PLS regression.
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References
L.B. Maher, “Personal genomes, the case of the missing heritability,” Nature, 456, 18–21, 2008.
T.A. Manolio, et al., “Finding the missing heritability of complex diseases” Nature, 461, 747–753, 2009.
R.A. Fisher, The Genetical Theory of Natural Selection, Oxford University Press, Oxford, 1930.
P.M. Visscher, W.G. Hill, and N. Wray, “Heritability in the Genomics era: Errors and misconceptions,” Nature Review Genetics, 9, 255–266, 2008.
G. Gibson, “Rare and common variants: twenty arguments,” Nature Review Genetics, 13, 135–145, 2012.
T. Hastie,T., R. Tibshirani, J.H., Friedman, The elements of Statistical Learning New York, Springer, 2008.
I. Frank, J. Friedman, “A statistical view of some Chemometrics regression tools,” Technometrics 35, 109–135, 1993.
L. Breiman, “Bagging Predictors” Machine Learning, 26, 123–140, 1996.
Y. Freund, R.E. Schapire, “A short introduction to boosting,” Journal of Japanese Society for Artificial Intelligence, 14, 771–780, 1999.
L. Breiman, “Random forests,” Machine Learning, 45, 5–32, 2001.
G.W. Brier, “Verification of forecasts expressed in terms of probability,” Monthly Weather Review, 78, 1–3, 1950.
E.M. Ohman, C.B. Granger, R.A. Harrington, K.L. Lee, “Risk stratification and therapeutic decision making in acute coronary syndromes,” The Journal of the American Medical Association, 284, 876–878, 2000.
J.A. Hanley, B.J. McNeil, “The meaning and use of the area under a receiver operating characteristic (ROC) curve,” Radiology, 143, 29–36, 1982.
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Ciampi, A., Yang, L., Labbe, A., Mérette, C. (2013). PLS Regression and Hybrid Methods in Genomics Association Studies. In: Abdi, H., Chin, W., Esposito Vinzi, V., Russolillo, G., Trinchera, L. (eds) New Perspectives in Partial Least Squares and Related Methods. Springer Proceedings in Mathematics & Statistics, vol 56. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8283-3_6
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DOI: https://doi.org/10.1007/978-1-4614-8283-3_6
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