CRP-Tree: a phylogenetic association test for binary traits
提出一种基于中国餐馆过程的二元性状进化模型，并推导出线性复杂度的系统发育关联检验方法，在剑尾鱼、乳腺癌、黄热病和甲型H1N1流感数据中验证了其效力优于其他方法。
Abstract An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples and it is usually estimated from molecular sequence data at a locus or from other type of genetic data. We propose a model for trait evolution inspired by the Chinese Restaurant Process that includes a parameter that controls the degree of preferential attachment, that is, the tendency of nodes in the tree to subtend from nodes of the same type. This model with no preferential attachment is equivalent to a structured coalescent model with simultaneous migration and coalescence events and serves as a null model. We derive a test for phylogenetic binary trait association with linear computational complexity and empirically demonstrate that it is more powerful than some other methods. We apply our test to study the phylogenetic association of some traits in swordtail fish, breast cancer, yellow fever virus, and influenza A H1N1 virus. R-package implementation of our methods is available at https://github.com/jyzhang27/CRPTree.