MiSPU
(Package: MiSPU) :
microbiome based sum of powered score (MiSPU)
We propose a class of microbiome based sum of powered score (MiSPU) tests based on a newly defined generalized taxon proportion that combines observed microbial composition information with phylogenetic tree information. Different from the existing methods, a MiSPU test is based on a weighted score of the generalized taxon proportion in a general framework of regression, upweighting more likely to be associated microbial lineages. Our simulations demonstrated that one or more MiSPU tests were more powerful than MiRKAT while correctly controlling type I error rates. An adaptive MiSPU (aMiSPU) test is proposed to combine multiple MiSPU tests with various weights, approximating the most powerful MiSPU for a given scenario, consequently being highly adaptive and high powered across various scenarios.
We used a phylogenetic tree of OTUs from a real throat microbiome data set, which consists of 856 OTUs after discarding singleton OTUs. Then based on a complicate statistical meodel, we generated the OTU counts for each individual to simulate the feature of real microbiome data.
There is an increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. In this package, we present a novel global testing method called aMiSPU, that is highly adaptive and thus high powered across various scenarios, alleviating the issue with the choice of a phylogenetic distance. Our simulations and real data analysis demonstrated that aMiSPU test was often more powerful than several competing methods while correctly controlling type I error rates.
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