Brief. Bioinformatics - Iteratively reweighted LASSO for mapping multiple quantitative trait loci.

Tópicos

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Resumo

The iteratively reweighted least square (IRLS) method is mostly identical to maximum likelihood (ML) method in terms of parameter estimation and power of quantitative trait locus (QTL) detection. But the IRLS is greatly superior to ML in terms of computing speed and the robustness of parameter estimation. In conjunction with the priors of parameters, ML can analyze multiple QTL model based on Bayesian theory, whereas under a single QTL model, IRLS has very limited statistical power to detect multiple QTLs. In this study, we proposed the iteratively reweighted least absolute shrinkage and selection operator (IRLASSO) for extending IRLS to simultaneously map multiple QTLs. The LASSO with coordinate descent step is employed to efficiently estimate non-zero genetic effect of each locus scanned over entire genome. Simulations demonstrate that IRLASSO has a higher precision of parameter estimation and power to detect QTL than IRLS, and is able to estimate residual variance more accurately than the unweighted LASSO based on LS. Especially, IRLASSO is very fast, usually taking less than five iterations to converge. The barley dataset from the North American Barley Genome Mapping Project is reanalyzed by our proposed method.

Resumo Limpo

iter reweight least squar irl method most ident maximum likelihood ml method term paramet estim power quantit trait locus qtl detect irl great superior ml term comput speed robust paramet estim conjunct prior paramet ml can analyz multipl qtl model base bayesian theori wherea singl qtl model irl limit statist power detect multipl qtls studi propos iter reweight least absolut shrinkag select oper irlasso extend irl simultan map multipl qtls lasso coordin descent step employ effici estim nonzero genet effect locus scan entir genom simul demonstr irlasso higher precis paramet estim power detect qtl irl abl estim residu varianc accur unweight lasso base ls especi irlasso fast usual take less five iter converg barley dataset north american barley genom map project reanalyz propos method

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