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Statistical Computing and Graphics

Facilitating the Calculation of the Efficient Score Using Symbolic Computing

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Pages 199-205 | Received 01 Feb 2017, Published online: 05 Jun 2018

References

  • Abecasis, G. R., Cardon, L. R., and Cookson, W. O. (2000), “A General Test of Association for Quantitative Traits in Nuclear Families,” The American Journal of Human Genetics, 66, 279–292.
  • Andrews, D. F., and Stafford, J. E. (2000), Symbolic Computation for Statistical Inference, New York: Oxford University Press.
  • Caviness, B. (1986), “Computer Algebra: Past and Future,” Journal of Symbolic Computation, 2, 217–236.
  • Conneely, K. N., and Boehnke, M. (2007), “So Many Correlated Tests, So Little Time! Rapid Adjustment of P Values for Multiple Correlated Tests,” The American Journal of Human Genetics, 81, 1158–1168.
  • Continuum Analytics (2016), “Anaconda Software Distribution, v2-2.4.0,” available at https://continuum.io.
  • Ekström Smedby, K., Lindgren, C. M., Hjalgrim, H., Humphreys, K., Schöllkopf, C., Chang, E. T., Roos, G., Ryder, L. P., Falk, K. I., Palmgren, J., Kere, J., Melbye, M., Glimelius, B., and Adami, H.-O. (2006), “Variation in DNA Repair Genes ERCC2, XRCC1, and XRCC3 and Risk of Follicular Lymphoma,” Cancer Epidemiology and Prevention Biomarkers, 15, 258–265.
  • Freedman, D. A. (2007), “How can the Score Test be Inconsistent?,” The American Statistician, 61, 291–295.
  • Freedman, N. D., Ahn, J., Hou, L., Lissowska, J., Zatonski, W., Yeager, M., Chanock, S. J., Chow, W. H., and Abnet, C. C. (2009), “Polymorphisms in Estrogen- and Androgen-metabolizing Genes and the Risk of Gastric Cancer,” Carcinogenesis, 30, 71–77.
  • Fulker, D., Cherny, S., Sham, P., and Hewitt, J. (1999), “Combined Linkage and Association Sib-pair Analysis for Quantitative Traits,” The American Journal of Human Genetics, 64, 259–267.
  • Gaudet, M. M., Kirchhoff, T., Green, T., Vijai, J., Korn, J. M., Guiducci, C., Segr, A. V., McGee, K., McGuffog, L., Kartsonaki, C., Morrison, J., Healey, S., Sinilnikova, O. M., Stoppa-Lyonnet, D., Mazoyer, S., Gauthier-Villars, M., Sobol, H., Longy, M., Frenay, M., Collaborators, G. S., Hogervorst, F. B. L., Rookus, M. A., Colle, J. M., Hoogerbrugge, N., van Roozendaal, K. E. P., Collaborators, H. S., Piedmonte, M., Rubinstein, W., Nerenstone, S., Van Le, L., Blank, S. V., Calds, T., de la Hoya, M., Nevanlinna, H., Aittomki, K., Lazaro, C., Blanco, I., Arason, A., Johannsson, O. T., Barkardottir, R. B., Devilee, P., Olopade, O. I., Neuhausen, S. L., Wang, X., Fredericksen, Z. S., Peterlongo, P., Manoukian, S., Barile, M., Viel, A., Radice, P., Phelan, C. M., Narod, S., Rennert, G., Lejbkowicz, F., Flugelman, A., Andrulis, I. L., Glendon, G., Ozcelik, H., OCGN, Toland, A. E., Montagna, M., D’Andrea, E., Friedman, E., Laitman, Y., Borg, A., Beattie, M., Ramus, S. J., Domchek, S. M., Nathanson, K. L., Rebbeck, T., Spurdle, A. B., Chen, X., Holland, H., kConFab, John, E. M., Hopper, J. L., Buys, S. S., Daly, M. B., Southey, M. C., Terry, M. B., Tung, N., Overeem Hansen, T. V., Nielsen, F. C., Greene, M. I., Mai, P. L., Osorio, A., Durn, M., Andres, R., Bentez, J., Weitzel, J. N., Garber, J., Hamann, U., Peock, S., Cook, M., Oliver, C., Frost, D., Platte, R., Evans, D. G., Lalloo, F., Eeles, R., Izatt, L., Walker, L., Eason, J., Barwell, J., Godwin, A. K., Schmutzler, R. K., Wappenschmidt, B., Engert, S., Arnold, N., Gadzicki, D., Dean, M., Gold, B., Klein, R. J., Couch, F. J., Chenevix-Trench, G., Easton, D. F., Daly, M. J., Antoniou, A. C., Altshuler, D. M., and Offit, K. (2010), “Common Genetic Variants and Modification of Penetrance of BRCA2-Associated Breast Cancer,” PLOS Genetics, 6, 1–12.
  • Hall, W. J., and Mathiason, D. J. (1990), “On Large-Sample Estimation and Testing in Parametric Models,” International Statistical Review/Revue Internationale de Statistique, 58, 77–97.
  • Helton, J. W., Miller, R. L., and Stankus, M. (1996), “NCAlgebra: A Mathematica Package for doing Noncommuting Algebra,” available at http://math.ucsd.edu/∼ncalg.
  • Horton, N. J., and Hardin, J. S. (2015), “Teaching the Next Generation of Statistics Students to Think with Data: Special Issue on Statistics and the Undergraduate Curriculum,” The American Statistician, 69, 259–265.
  • Jiang, Y., Ji, Y., Sibley, A. B., Li, Y.-J., and Allen, A. S. (2017), “Leveraging Population Information in Family-Based Rare Variant Association Analyses of Quantitative Traits,” Genetic Epidemiology, 41, 98–107.
  • Lin, D. Y. (2005), “An Efficient Monte Carlo Approach to Assessing Statistical Significance in Genomic Studies,” Bioinformatics, 21, 781.
  • Magnus, J. R., and Neudecker, H. (2007), Matrix Differential Calculus with Applications in Statistics and Econometrics (3rd ed.), Chichester, UK: Wiley.
  • Maplesoft, a division of Waterloo Maple Inc. (2014), Maple v18.0, Waterloo, Ontario: Springer Science+Business Media, LLC.
  • Maxima (2016), “Maxima, a Computer Algebra System, v5.39.0,” available at http://maxima.sourceforge.net/.
  • Moses, J. (2012), “Macsyma: A Personal History,” Journal of Symbolic Computation, 47, 78–84.
  • Pang, H., Kim, I., and Zhao, H. (2015), “Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data,” Statistics in Biosciences, 7, 167–186.
  • Poore, G. M. (2013), “Reproducible Documents with PythonTeX,” Proceedings of the 12th Python in Science Conference, pp. 123–130.
  • Rao, C. R. (1948), “Tests of Significance in Multivariate Analysis,” Biometrika, 35, 58–79.
  • Schaffner, S., Foo, C., Gabriel, S., Reich, D., Daly, M., and Altshuler, D. (2005), “Calibrating a Coalescent Simulation of Human Genome Sequence Variation,” Genome Research, 15, 1576–1583.
  • Seaman, S., and Müller-Myhsok, B. (2005), “Rapid Simulation of p Values for Product Methods and Multiple-Testing Adjustment in Association Studies,” The American Journal of Human Genetics, 76, 399–408.
  • Siamakpour-Reihani, S., Owzar, K., Jiang, C., Scarbrough, P. M., Craciunescu, O. I., Horton, J. K., Dressman, H. K., Blackwell, K. L., and Dewhirst, M. W. (2015), “Genomic Profiling in Locally Advanced and Inflammatory Breast Cancer and its Link to DCE-MRI and Overall Survival,” International Journal of Hyperthermia, 31, 386–395.
  • Sibley, A. B., Li, Z., Jiang, Y., Chan, C., Allen, A., and Owzar, K. (2014), “Facilitating the Calculation of the Efficient Score Using Symbolic Computing,” in JSM Proceedings, Section on Statistical Education, Alexandria, VA: American Statistical Association, pp. 3136–3143.
  • Sorensen, D., and Gianola, D. (2013), Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics, New York: Springer-Verlag New York Inc.
  • SymPy Development Team (2014), “Sympy: Python Library for Symbolic Mathematics,” available at http://www.sympy.org.
  • The Sage Developers (2017), “SageMath, the Sage Mathematics Software System, v7.6,” available at http://www.sagemath.org.
  • Tsiatis, A. A. (2006), Semiparametric Theory and Missing Data, New York: Springer Science+Business Media, LLC.
  • Wolfram Research, Inc. (2012), Mathematica v9.0, Champaign, IL: Wolfram Research, Inc.
  • Zhang, X., Johnson, A. D., Hendricks, A. E., Hwang, S.-J., Tanriverdi, K., Ganesh, S. K., Smith, N. L., Peyser, P. A., Freedman, J. E., and O’Donnell, C. J. (2014), “Genetic Associations with Expression for Genes Implicated in GWAS Studies for Atherosclerotic Cardiovascular Disease and Blood Phenotypes,” Human Molecular Genetics, 23, 782.

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