IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v12y2013i4p433-448n2.html
   My bibliography  Save this article

The mid p-value in exact tests for Hardy-Weinberg equilibrium

Author

Listed:
  • Graffelman Jan

    (Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, 08028 Barcelona, Spain)

  • Moreno Victor

    (Cancer Prevention Program, Catalan Institute of Oncology (ICO) Bellvitge Biomedical Research Institute (IDIBELL), Faculty of Medicine and CIBERESP, Department of Clinical Sciences, University of Barcelona (UB), Gran Via 199, 08908 L’Hospitalet del Llobregat (Barcelona), Spain)

Abstract

Objective: Exact tests for Hardy-Weinberg equilibrium are widely used in genetic association studies. We evaluate the mid p-value, unknown in the genetics literature, as an alternative for the standard p-value in the exact test.Method: The type 1 error rate and the power of the exact test are calculated for different sample sizes, sigificance levels, minor allele counts and degrees of deviation from equilibrium. Three different p-value are considered: the standard two-sided p-value, the doubled one-sided p-value and the mid p-value. Practical implications of using the mid p-value are discussed with HapMap datasets and a data set on colon cancer.Results: The mid p-value is shown to have a type 1 error rate that is always closer to the nominal level, and to have better power. Differences between the standard p-value and the mid p-value can be large for insignificant results, and are smaller for significant results. The analysis of empirical databases shows that the mid p-value uncovers more significant markers, and that the equilibrium null distribution is not tenable for both databases.Conclusion: The standard exact p-value is overly conservative, in particular for small minor allele frequencies. The mid p-value ameliorates this problem by bringing the rejection rate closer to the nominal level, at the price of ocasionally exceeding the nominal level.

Suggested Citation

  • Graffelman Jan & Moreno Victor, 2013. "The mid p-value in exact tests for Hardy-Weinberg equilibrium," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(4), pages 433-448, August.
    • Handle: RePEc:bpj:sagmbi:v:12:y:2013:i:4:p:433-448:n:2
    DOI: 10.1515/sagmb-2012-0039
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2012-0039
    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-2012-0039?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. Jon Wakefield, 2010. "Bayesian Methods for Examining Hardy–Weinberg Equilibrium," Biometrics, The International Biometric Society, vol. 66(1), pages 257-265, March.
    2. Attia John & Thakkinstian Ammarin & McElduff Patrick & Milne Elizabeth & Dawson Somer & Scott Rodney J & Klerk Nicholas de & Armstrong Bruce & Thompson John, 2010. "Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-17, January.
    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. Jan Graffelman & Milagros Sánchez & Samantha Cook & Victor Moreno, 2013. "Statistical Inference for Hardy-Weinberg Proportions in the Presence of Missing Genotype Information," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-11, December.
    2. Brentani Helena & Nakano Eduardo Y & Martins Camila B & Izbicki Rafael & Pereira Carlos Alberto, 2011. "Disequilibrium Coefficient: A Bayesian Perspective," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, May.

    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:12:y:2013:i:4:p:433-448: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.