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Genome-wide Association Studies: Controlling False Discovery Rate using Knockoffs

Kafi, Mahdi | 2024

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 56996 (19)
  4. University: Sharif University of Technology
  5. Department: Computer Engineering
  6. Advisor(s): Motahari, Abolfazl
  7. Abstract:
  8. In recent years, with the advancement of genetics technologies, many data from this field have been made available to researchers. Therefore, many analytical problems have been defined for these data. Genome-wide association studies, or GWAS for short, is one of these issues that deals with finding genetic positions affecting traits or diseases. Common approaches to this problem either examine genetic variants one by one or fail to consider the specific structure of genetic data. Also, both mentioned approaches do not provide a guarantee to control the rate of false positives. In this thesis, an attempt has been made to propose a method to solve the GWAS problem by using the new statistical framework called knockoff and its improvements. The proposed method, using two previous researches that have recently been proposed, can identify and report the variants and groups of variants that are causal in the phenotype, according to the structure of the genetic data. This method, named Derandomized-KnockoffZoom, has adequate statistical power and also ensures the control of false discovery rate. In addition, the findings of this method are up to ten percent more reproducible than the previous method, or in other words, its findings do not differ much in different executions on the same data
  9. Keywords:
  10. False Discovery Rate ; Conditional Independence ; Knockoff Framework ; Genome-Wide Asocciation Studies (GWAS)

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