{"@context":"http://iiif.io/api/presentation/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/manifest.json","@type":"sc:Manifest","label":"Constrained Functional Linear Model for Multi-loci Genetic Mapping","metadata":[{"label":"dc.description.sponsorship","value":"This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree."},{"label":"dc.format","value":"Monograph"},{"label":"dc.format.medium","value":"Electronic Resource"},{"label":"dc.identifier.uri","value":"http://hdl.handle.net/11401/77676"},{"label":"dc.language.iso","value":"en_US"},{"label":"dc.publisher","value":"The Graduate School, Stony Brook University: Stony Brook, NY."},{"label":"dcterms.abstract","value":"In genome-wide association studies (GWAS), the efficient incorporation of linkage disequilibria (LD) among dense-typed linked genetic variants into analysis to improve the association power is critical yet challenging problem. Functional linear models (FLM), which impose a smoothing structure on the coefficients of correlated covariates, are advantageous in genetic mapping of multiple variants with high LD. Here we propose a novel constrained FLM (cFLM) framework to perform simultaneous association tests on a block of linked SNPs with various traits, including continuous, binary and zero-inflated count phenotypes. The new cFLM applies a set of inequality constraints on the FLM to ensure model identifiability under different genetic codings. The method is implemented via B-splines, with an augmented Lagrangian algorithm is employed for parameter estimation. For hypotheses testing, a test statistic that accounts for the model constraints has been derived, following a mixture of chi-square distributions. Simulation results show that cFLM is effective in identifying causal loci and gene clusters compared to several competing methods based on single markers and SKAT-C. We applied the proposed method to analyze the COGEND data and a large-scale GWAS data on dental caries risk."},{"label":"dcterms.available","value":"2017-09-20T16:53:18Z"},{"label":"dcterms.contributor","value":"Wu, Song"},{"label":"dcterms.creator","value":"Huang, Jiayu"},{"label":"dcterms.dateAccepted","value":"2017-09-20T16:53:18Z"},{"label":"dcterms.dateSubmitted","value":"2017-09-20T16:53:18Z"},{"label":"dcterms.description","value":"Department of Applied Mathematics and Statistics."},{"label":"dcterms.extent","value":"117 pg."},{"label":"dcterms.format","value":"Monograph"},{"label":"dcterms.identifier","value":"http://hdl.handle.net/11401/77676"},{"label":"dcterms.issued","value":"2016-12-01"},{"label":"dcterms.language","value":"en_US"},{"label":"dcterms.provenance","value":"Made available in DSpace on 2017-09-20T16:53:18Z (GMT). No. of bitstreams: 1\nHuang_grad.sunysb_0771E_12691.pdf: 5447699 bytes, checksum: e926cf721e6b81ba9022a4877f8dc638 (MD5)\n Previous issue date: 1"},{"label":"dcterms.publisher","value":"The Graduate School, Stony Brook University: Stony Brook, NY."},{"label":"dcterms.subject","value":"Statistics"},{"label":"dcterms.title","value":"Constrained Functional Linear Model for Multi-loci Genetic Mapping"},{"label":"dcterms.type","value":"Dissertation"},{"label":"dc.type","value":"Dissertation"}],"description":"This manifest was generated dynamically","viewingDirection":"left-to-right","sequences":[{"@type":"sc:Sequence","canvases":[{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json","@type":"sc:Canvas","label":"Page 1","height":1650,"width":1275,"images":[{"@type":"oa:Annotation","motivation":"sc:painting","resource":{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/86%2F63%2F16%2F8663168395353526284928621074842648039/full/full/0/default.jpg","@type":"dctypes:Image","format":"image/jpeg","height":1650,"width":1275,"service":{"@context":"http://iiif.io/api/image/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/86%2F63%2F16%2F8663168395353526284928621074842648039","profile":"http://iiif.io/api/image/2/level2.json"}},"on":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json"}]}]}]}