IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v16y2017i3p189-198n2.html
   My bibliography  Save this article

Genetic association test based on principal component analysis

Author

Listed:
  • Chen Zhongxue

    (Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. 7th Street, Bloomington, IN 47405, USA)

  • Han Shizhong

    (Department of Psychiatry, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA)

  • Wang Kai

    (Department of Biostatistics, N322 CPHB College of Public Health, University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA)

Abstract

Many gene- and pathway-based association tests have been proposed in the literature. Among them, the SKAT is widely used, especially for rare variants association studies. In this paper, we investigate the connection between SKAT and a principal component analysis. This investigation leads to a procedure that encompasses SKAT as a special case. Through simulation studies and real data applications, we compare the proposed method with some existing tests.

Suggested Citation

  • Chen Zhongxue & Han Shizhong & Wang Kai, 2017. "Genetic association test based on principal component analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(3), pages 189-198, August.
    • Handle: RePEc:bpj:sagmbi:v:16:y:2017:i:3:p:189-198:n:2
    DOI: 10.1515/sagmb-2016-0061
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2016-0061
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2016-0061?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Chen, Zhongxue, 2013. "Association tests through combining p-values for case control genome-wide association studies," Statistics & Probability Letters, Elsevier, vol. 83(8), pages 1854-1862.
    2. Chen, Zhongxue & Nadarajah, Saralees, 2014. "On the optimally weighted z-test for combining probabilities from independent studies," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 387-394.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Chen, Zhongxue & Huang, Hanwen & Ng, Hon Keung Tony, 2014. "An improved robust association test for GWAS with multiple diseases," Statistics & Probability Letters, Elsevier, vol. 91(C), pages 153-161.
    2. Gelio Alves & Yi-Kuo Yu, 2014. "Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-11, March.
    3. Hong Zhang & Zheyang Wu, 2023. "The generalized Fisher's combination and accurate p‐value calculation under dependence," Biometrics, The International Biometric Society, vol. 79(2), pages 1159-1172, June.
    4. Chien Li-Chu, 2020. "Combining dependent p-values by gamma distributions," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 19(4-6), pages 1-12, December.
    5. Chen, Zhongxue & Nadarajah, Saralees, 2014. "On the optimally weighted z-test for combining probabilities from independent studies," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 387-394.
    6. Ashes Banerjee & Srinivas Pasupuleti & Mritunjay Kumar Singh & G.N. Pradeep Kumar, 2018. "An Investigation of Parallel Post-Laminar Flow through Coarse Granular Porous Media with the Wilkins Equation," Energies, MDPI, vol. 11(2), pages 1-19, February.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:16:y:2017:i:3:p:189-198:n:2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.