An Adaptive and Robust Test for Microbial Community Analysis
In microbiome studies, researchers measure the abundance of each operational taxon unit (OTU) and are often interested in testing the association between the microbiota and the clinical outcome while conditional on certain covariates. Two types of approaches exists for this testing purpose: the OTU-...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.846258/full |
| _version_ | 1828347743726206976 |
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| author | Qingyu Chen Shili Lin Chi Song |
| author_facet | Qingyu Chen Shili Lin Chi Song |
| author_sort | Qingyu Chen |
| collection | DOAJ |
| description | In microbiome studies, researchers measure the abundance of each operational taxon unit (OTU) and are often interested in testing the association between the microbiota and the clinical outcome while conditional on certain covariates. Two types of approaches exists for this testing purpose: the OTU-level tests that assess the association between each OTU and the outcome, and the community-level tests that examine the microbial community all together. It is of considerable interest to develop methods that enjoy both the flexibility of OTU-level tests and the biological relevance of community-level tests. We proposed MiAF, a method that adaptively combines p-values from the OTU-level tests to construct a community-level test. By borrowing the flexibility of OTU-level tests, the proposed method has great potential to generate a series of community-level tests that suit a range of different microbiome profiles, while achieving the desirable high statistical power of community-level testing methods. Using simulation study and real data applications in a smoker throat microbiome study and a HIV patient stool microbiome study, we demonstrated that MiAF has comparable or better power than methods that are specifically designed for community-level tests. The proposed method also provides a natural heuristic taxa selection. |
| first_indexed | 2024-04-14T00:44:49Z |
| format | Article |
| id | doaj.art-00472cf8ae414ffcb3f07eb1388906de |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-14T00:44:49Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-00472cf8ae414ffcb3f07eb1388906de2022-12-22T02:22:03ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-05-011310.3389/fgene.2022.846258846258An Adaptive and Robust Test for Microbial Community AnalysisQingyu Chen0Shili Lin1Chi Song2Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, United StatesDepartment of Statistics, College of Arts and Sciences, The Ohio State University, Columbus, OH, United StatesDivision of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, United StatesIn microbiome studies, researchers measure the abundance of each operational taxon unit (OTU) and are often interested in testing the association between the microbiota and the clinical outcome while conditional on certain covariates. Two types of approaches exists for this testing purpose: the OTU-level tests that assess the association between each OTU and the outcome, and the community-level tests that examine the microbial community all together. It is of considerable interest to develop methods that enjoy both the flexibility of OTU-level tests and the biological relevance of community-level tests. We proposed MiAF, a method that adaptively combines p-values from the OTU-level tests to construct a community-level test. By borrowing the flexibility of OTU-level tests, the proposed method has great potential to generate a series of community-level tests that suit a range of different microbiome profiles, while achieving the desirable high statistical power of community-level testing methods. Using simulation study and real data applications in a smoker throat microbiome study and a HIV patient stool microbiome study, we demonstrated that MiAF has comparable or better power than methods that are specifically designed for community-level tests. The proposed method also provides a natural heuristic taxa selection.https://www.frontiersin.org/articles/10.3389/fgene.2022.846258/fullhuman microbiomeassociation testcommunity-level testOTU-level testadaptive combination of p-values |
| spellingShingle | Qingyu Chen Shili Lin Chi Song An Adaptive and Robust Test for Microbial Community Analysis Frontiers in Genetics human microbiome association test community-level test OTU-level test adaptive combination of p-values |
| title | An Adaptive and Robust Test for Microbial Community Analysis |
| title_full | An Adaptive and Robust Test for Microbial Community Analysis |
| title_fullStr | An Adaptive and Robust Test for Microbial Community Analysis |
| title_full_unstemmed | An Adaptive and Robust Test for Microbial Community Analysis |
| title_short | An Adaptive and Robust Test for Microbial Community Analysis |
| title_sort | adaptive and robust test for microbial community analysis |
| topic | human microbiome association test community-level test OTU-level test adaptive combination of p-values |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.846258/full |
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