IDEAS home Printed from https://ideas.repec.org/a/bla/jorssc/v48y1999i1p53-61.html
   My bibliography  Save this article

Fitting Markov chain models to discrete state series such as DNA sequences

Author

Listed:
  • P. J. Avery
  • D. A. Henderson

Abstract

Discrete state series such as DNA sequences can often be modelled by Markov chains. The analysis of such series is discussed in the context of log‐linear models. The data produce contingency tables with similar margins due to the dependence of the observations. However, despite the unusual structure of the tables, the analysis is equivalent to that for data from multinomial sampling. The reason why the standard number of degrees of freedom is correct is explained by using theoretical arguments and the asymptotic distribution of the deviance is verified empirically. Problems involved with fitting high order Markov chain models, such as reduced power and computational expense, are also discussed.

Suggested Citation

  • P. J. Avery & D. A. Henderson, 1999. "Fitting Markov chain models to discrete state series such as DNA sequences," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 48(1), pages 53-61.
    • Handle: RePEc:bla:jorssc:v:48:y:1999:i:1:p:53-61
    DOI: 10.1111/1467-9876.00139
    as

    Download full text from publisher

    File URL: https://doi.org/10.1111/1467-9876.00139
    Download Restriction: no
    File URL: https://libkey.io/10.1111/1467-9876.00139?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
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. repec:aaa:journl:v:3:y:1999:i:1:p:87-100 is not listed on IDEAS
    2. Jonsson, Robert, 2011. "A Markov Chain Model for Analysing the Progression of Patient’s Health States," Research Reports 2011:6, University of Gothenburg, Statistical Research Unit, School of Business, Economics and Law.
    3. Gabadinho, Alexis & Ritschard, Gilbert, 2016. "Analyzing State Sequences with Probabilistic Suffix Trees: The PST R Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 72(i03).
    4. J. Besag & D. Mondal, 2013. "Exact Goodness-of-Fit Tests for Markov Chains," Biometrics, The International Biometric Society, vol. 69(2), pages 488-496, June.
    5. M. L. Menéndez & L. Pardo & M. C. Pardo & K. Zografos, 2011. "Testing the Order of Markov Dependence in DNA Sequences," Methodology and Computing in Applied Probability, Springer, vol. 13(1), pages 59-74, March.
    6. Jonsson, Robert, 2011. "Tests of Markov Order and Homogeneity in a Markov Chain," Research Reports 2011:7, University of Gothenburg, Statistical Research Unit, School of Business, Economics and Law.
    7. Anastasios N. Arapis & Frosso S. Makri & Zaharias M. Psillakis, 2017. "Joint distribution of k-tuple statistics in zero-one sequences of Markov-dependent trials," Journal of Statistical Distributions and Applications, Springer, vol. 4(1), pages 1-13, December.
    8. Varin, Cristiano & Vidoni, Paolo, 2006. "Pairwise likelihood inference for ordinal categorical time series," Computational Statistics & Data Analysis, Elsevier, vol. 51(4), pages 2365-2373, December.

    More about this item

    Statistics

    Access and download statistics

    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:bla:jorssc:v:48:y:1999:i:1:p:53-61. 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.

    We have no bibliographic references for this item. You can help adding them by using 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: Wiley Content Delivery (email available below). General contact details of provider: https://edirc.repec.org/data/rssssea.html .

    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.