We have developed the SVSI package that attempts to test genetic associations with complex phenotypes such as ordered categorical phenotype or binary phenotype based on set-valued model and using a novel Set-Valued System Identification algorithm. The set-valued model models the classification/dichotomization process of a continuous complicated unobserved or unobervalble phenotype and models the relationship between categorical outcome and genetic variants. Set-Valued System Identification (SVSI) algorithm is a new algorithm based on expectation-maximization (EM) which has been proposed and appears in a wide range of applications such as sensor networks and telecommunications. The method is being published by Kang G et al (2014) in Annals of Human Genetics.
The method is implemented in SVSI R package written for the freely available statistical computing language R.
To Install SVSI:
More questions? Contact Guolian Kang.