gemma2 - GEMMA Multivariate Linear Mixed Model
Fits a multivariate linear mixed effects model that uses a polygenic term, after Zhou & Stephens (2014) (<https://www.nature.com/articles/nmeth.2848>). Of particular interest is the estimation of variance components with restricted maximum likelihood (REML) methods. Genome-wide efficient mixed-model association (GEMMA), as implemented in the package 'gemma2', uses an expectation-maximization algorithm for variance components inference for use in quantitative trait locus studies.
Last updated 4 years ago
em-algorithmgeneticsmixed-models
5.29 score 13 stars 1 dependents 10 scripts 174 downloadsqtl2pleio - Testing Pleiotropy in Multiparental Populations
We implement an adaptation of Jiang & Zeng's (1995) <https://www.genetics.org/content/140/3/1111> likelihood ratio test for testing the null hypothesis of pleiotropy against the alternative hypothesis, two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) <https://www.genetics.org/content/140/3/1111> and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in that our test accommodates multiparental populations.
Last updated 4 years ago
multiparental-populationsquantitative-geneticsquantitative-traitcpp
4.41 score 5 stars 26 scripts 230 downloads