An expectation-maximization algorithm for the Lasso estimation of quantitative trait locus effects

Heredity

Volumn 105, Issue 5, 2010, Pages 483-494

  Xu, S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Empirical Bayes; Lasso; mixed model; QTL mapping; shrinkage estimation

Indexed keywords

ALGORITHM; BAYESIAN ANALYSIS; EMPIRICAL ANALYSIS; GENOTYPE; LIFE HISTORY TRAIT; REGRESSION ANALYSIS;

ALGORITHM; ALLELE; ARTICLE; QUANTITATIVE TRAIT LOCUS; THEORETICAL MODEL;

ALGORITHMS; ALLELES; MODELS, THEORETICAL; QUANTITATIVE TRAIT LOCI;

EID: 77958485202     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2009.180     Document Type: Article

References (22)

1. Broman KW, Speed TP (2002). A model selection approach for the identification of quantitative trait loci in experimental crosses. J R Stat Soc Series B 64: 641-656.
2. Dempster AP, Laird NM, Rubin DB (1977). Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc B 39: 1-38.
3. Figueiredo MAT (2003). Adaptive sparseness for supervised learning. IEEE Trans Pattern Anal Mach Intell 25: 1151-1159.
4. Giri NC (1996). Multivariate Statistical Analysis. Marcel Dekker Inc: New York. pp 53-63.
5. Han L, Xu S (2008). A Fisher scoring algorithm for the weighted regression method of QTL mapping. Heredity 101: 453-464.
6. Hoerl AE, Kennard RW (1970). Ridge regression: Application to nonorthogonal problems. Technometrics 12: 68-82.
7. Lan H, Chen M, Flowers JB, Yandell BS, Stapleton DS, Mata CM et al. (2006). Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genet 2: E6.
8. Lan H, Stoehr JP, Nadler ST, Schueler KL, Yandell BS, Attie AD (2003). Dimension reduction for mapping mRNA abundance as quantitative traits. Genetics 164: 1607-1614.
9. Lindstrom MJ, Bates DM (1988). Newton-Raphson and EM algorithms for linear mixed-effects models for repeatedmeasures data. J Am Stat Assoc 83: 1014-1022.
10. Loudet O, Chaillou S, Camilleri C, Bouchez D, Daniel-Vedele F (2002). Bay-0 x Shahdara recombinant inbred line population: A powerful tool for the genetic dissection of complex traits in Arabidopsis. Theor Appl Genet 104: 1173-1184.
11. Manichaikul A, Moon JY, Sen S, Yandell BS, Broman KW (2009). A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics 181: 1077-1086.
12. Nelder JA, Mead R (1965). A simplex method for function minimization. Comput J 7: 308-313.
13. Park T, Casella G (2008). The Bayesian Lasso. J Am Stat Assoc 103: 681-686.
14. ter Braak CJ, Boer MP, Bink MC (2005). Extending Xu's Bayesian model for estimating polygenic effects using markers of the entire genome. Genetics 170: 1435-1438.
15. Tibshirani R (1996). Regression shrinkage and selection via the Lasso. J R Stat Soc Series B 58: 267-288.
16. Wang H, Zhang Y, Li X, Masinde GL, Mohan S, Baylink DJ et al. (2005). Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170: 465-480.
17. Whittaker JC, Thompson R, Denham MC (2000). Markerassisted selection using ridge regression. Genet Res 75: 249-252.
18. Xu S (1998). Iteratively reweighted least squares mapping of quantitative trait loci. Behav Genet 28: 341-355.
19. Xu S (2003). Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
20. Xu S (2007). An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 63: 513-521.
21. Yi N, Xu S (2008). Bayesian LASSO for quantitative trait loci mapping. Genetics 179: 1045-1055.
22. Yi N, Banerjee S (2009). Hierarchical generalized linear models for multiple quantitative trait locus mapping. Genetics 181: 1101-1113.