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ViewPoint and ViewDist: Utilities for Rapid Graphing of Linkage Distributions and Identification of Outliers

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Abstract

ViewPoint and ViewDist are standalone Java utilities designed to provide an interactive visual representation of data from files which may be created by the user or produced directly from analyses packages such as Mx. ViewPoint is designed for representation of linkage results and can be used for summarizing multiple univariate linkage results or providing detailed comparison of univariate and multivariate results, with optional dynamic sub-plots designed to display the QTL path coefficients at each marker. ViewDist is an easy to use distribution plotter designed for use with raw data or case-wise likelihood statistics. The utility can produce Q–Q plots (assuming either normal or χ2-distributions) and by allowing data to be read simultaneously from two files readily produces difference plots allowing comparison of the case-wise likelihood under two competing models.

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References

  • Lander E., Kruglyak L. (1995). Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat. Genet. 11: 241–247.

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  • Neale, M. C., Boker, S. M., Xie, G., and Maes, H. H. (2002). Mx: Statistical Modeling (6th ed.), VCU Box 900126, Richmond, VA 23298 http://www.vcu.edu/mx/: Department of Psychiatry.

  • SourceForge JSci Science API for Java 2005; an Open Source library of mathematical and scientific functions – website: http://www.sourceforge.net/projects/jsci

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Acknowledgments

The authors wish to acknowledge the support and helpful suggestions of David Duffy and Michael Neale. In addition, the authors would like to thank the staff and students of the Genetic Epidemiology Laboratory of the Queensland Institute of Medical Research, and in particular Narelle Hansell and Manuel Ferriera, for their comments, suggestions and testing throughout the development of these utilities.

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Authors and Affiliations

  1. Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Brisbane, Australia

    Harry N. Beeby, Sarah E. Medland & Nicholas G. Martin

  2. Cognitive Psychophysiology Laboratory, University of Queensland, Toowoomba, Australia

    Sarah E. Medland

  3. Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Brisbane, 4029, Australia

    Harry N. Beeby

Authors
  1. Harry N. Beeby
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  2. Sarah E. Medland
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  3. Nicholas G. Martin
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Corresponding author

Correspondence to Harry N. Beeby.

Appendix A. Syntax for Running ViewPoint and ViewDist from the Command Prompt

Appendix A. Syntax for Running ViewPoint and ViewDist from the Command Prompt

  • ViewPoint

  • java -jar ViewPoint.jar

  •  [-infile <input data filename>]

  •  [-suggestive <suggestive score threshold (float)>]

  •  [-significant <significant score threshold (float)>]

  •  [-fixXaxis (X axis units set to max chromo length)]

  •  [-plot <plot type U or M>]

  •  [-help (usage)]

  • ViewDist

  • java -jar ViewDist.jar

  •  [-infile <input data filename>]

  •  [-diffile1 <first difference filename>]

  •  [-diffile2 <second difference filename>]

  •  [-infoCol <info column number>]

  •  [-scorecol <score column number>]

  •  [-intObsCol <observation count column number>]

  •  [-intModelCol <model column number>]

  •  [-plottype <plot type: internal, normal, chi>]

  •  [-help (usage)]

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Beeby, H.N., Medland, S.E. & Martin, N.G. ViewPoint and ViewDist: Utilities for Rapid Graphing of Linkage Distributions and Identification of Outliers. Behav Genet 36, 7–11 (2006). https://doi.org/10.1007/s10519-006-9045-z

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  • DOI: https://doi.org/10.1007/s10519-006-9045-z

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