全因子分析:一个用于分析全因子交配设计中遗传和母体方差成分的R包。
fullfact: an R package for the analysis of genetic and maternal variance components from full factorial mating designs.
作者信息
Houde Aimee Lee S, Pitcher Trevor E
机构信息
Department of Biological Sciences University of Windsor Windsor Ontario N9B 3P4 Canada; Great Lakes Institute for Environmental Research University of Windsor Windsor Ontario N9B 3P4 Canada.
出版信息
Ecol Evol. 2016 Feb 14;6(6):1656-65. doi: 10.1002/ece3.1943. eCollection 2016 Mar.
Full factorial breeding designs are useful for quantifying the amount of additive genetic, nonadditive genetic, and maternal variance that explain phenotypic traits. Such variance estimates are important for examining evolutionary potential. Traditionally, full factorial mating designs have been analyzed using a two-way analysis of variance, which may produce negative variance values and is not suited for unbalanced designs. Mixed-effects models do not produce negative variance values and are suited for unbalanced designs. However, extracting the variance components, calculating significance values, and estimating confidence intervals and/or power values for the components are not straightforward using traditional analytic methods. We introduce fullfact - an R package that addresses these issues and facilitates the analysis of full factorial mating designs with mixed-effects models. Here, we summarize the functions of the fullfact package. The observed data functions extract the variance explained by random and fixed effects and provide their significance. We then calculate the additive genetic, nonadditive genetic, and maternal variance components explaining the phenotype. In particular, we integrate nonnormal error structures for estimating these components for nonnormal data types. The resampled data functions are used to produce bootstrap-t confidence intervals, which can then be plotted using a simple function. We explore the fullfact package through a worked example. This package will facilitate the analyses of full factorial mating designs in R, especially for the analysis of binary, proportion, and/or count data types and for the ability to incorporate additional random and fixed effects and power analyses.
完全析因育种设计对于量化解释表型性状的加性遗传方差、非加性遗传方差和母体方差的量很有用。这种方差估计对于检验进化潜力很重要。传统上,完全析因交配设计是使用双向方差分析进行分析的,这可能会产生负方差值,并且不适用于不平衡设计。混合效应模型不会产生负方差值,并且适用于不平衡设计。然而,使用传统分析方法提取方差分量、计算显著性值以及估计分量的置信区间和/或功效值并非易事。我们引入了fullfact——一个R包,它解决了这些问题,并便于使用混合效应模型对完全析因交配设计进行分析。在这里,我们总结了fullfact包的功能。观测数据函数提取由随机效应和固定效应解释的方差,并提供它们的显著性。然后,我们计算解释表型的加性遗传方差、非加性遗传方差和母体方差分量。特别是,我们整合了非正态误差结构来估计非正态数据类型的这些分量。重采样数据函数用于生成自助t置信区间,然后可以使用一个简单函数进行绘制。我们通过一个实例来探索fullfact包。这个包将便于在R中对完全析因交配设计进行分析,特别是对于二元、比例和/或计数数据类型的分析,以及纳入额外随机效应和固定效应以及功效分析的能力。