performance of penalized maximum likelihood in estimation of genetic covariances matrices处罚的性能极大似然估计的遗传协方差矩阵.pdf

Meyer Genetics Selection Evolution 2011, 43:39 Ge n e t i c s /content/43/1/39 Se l e c t i o n Evolution RESEARCH Open Access Performance of penalized maximum likelihood in estimation of genetic covariances matrices Karin Meyer Abstract Background: Estimation of genetic covariance matrices for multivariate problems comprising more than a few traits is inherently problematic, since sampling variation increases dramatically with the number of traits. This paper investigates the efficacy of regularized estimation of covariance components in a maximum likelihood framework, imposing a penalty on the likelihood designed to reduce sampling variation. In particular, penalties that “borrow strength” from the phenotypic covariance matrix are considered. Methods: An extensive simulation study was carried out to investigate the reduction in average ‘loss’, i.e. the deviation in estimated matrices from the population values, and the accompanying bias for a range of parameter values and sample sizes. A number of penalties are examined, penalizing either the canonical eigenvalues or the genetic covariance or correlation matrices. In addition, several strategies to determine the amount of penalization to be applied, i.e. to estimate the appropriate tuning factor, are explored. Results: It is shown that substantial reductions in loss for estimates of genetic covariance can be achieved for small to moderate sample sizes. While no penalty performed best overall, penalizing the variance among the estimated canonical eigenvalues on the logarithmic sc