Genetic association studies

• Code for fitting an ultra-sparse variational Bayes spike regression model, with applications to Genome-wide association studies (vBsr) is here. WARNING: Code is in an early release form (version 0.0.1), and details of the model are forthcoming.
• Code for approximate power calculations for identification of gene x gene and gene x environment interactions in genomewide association studies using a two-stage analysis. Download the package powerGWASinteraction from CRAN.
  • This method is described in C. Kooperberg and M. LeBlanc (2008). Increasing the power of identifying gene x gene interactions in genome-wide association studies Genetic Epidemiology, 32, 255-263.
• Code for SNP-Haplotype Adaptive Regression (SHARE) to perform multi-locus analysis in order to account for LD patterns observed in human genome developed by James Dai is available in the package SHARE from CRAN.
  • This method is described in J. Y. Dai, M. LeBlanc, N. L. Smith, B. Psaty and C. Kooperberg (2009). SHARe: an algorithm to select the most informative set of SNPs for candidate genetic association. Biostatistics, 10, 680-693.
• Code for semiparametric estimation exploiting covariate independence in two-phase randomized trials developed by James Dai is available in the package TwoPhaseInd from CRAN.
  • This method is described in J. Y. Dai, M. LeBlanc, and C. Kooperberg (2009). Semiparametric estimation exploiting covariate independence in two-phase randomized trials. Biometrics, 65, 178-187.

Logic Regression

Logic Regression
Logic Regression: R libraries to fit logic regression models.

• The Logic regression program is described in Ingo Ruczinski, Charles Kooperberg, and Michael L. LeBlanc (2003). Logic Regression. Journal of Computational and Graphical Statistics, 12, 475-511.
• Extensions are discussed in Charles Kooperberg and Ingo Ruczinski. Identifying interacting SNPs using Monte Carlo Logic Regression. Genetic Epidemiology, 28 , 157-170.

Microarrays

• Improved background correction for spotted DNA microarrays is implemented in Gordon Smyth: R code. It is also implemented in Gordon Smyth's Limma package on bioconductor as the function kooperberg.
  • This method is described in C. Kooperberg, T. G. Fazzio, J. J. Delrow, and T. Tskuiyama (2002) Improved background correction for spotted DNA microarrays Journal of Computational Biology, 9, 55-66.

Polynomial Splines

Libraries

• Software for hare, heft, lspec, logspline, polyclass and polymars, as well as the logspline version discussed in Stone et al (1997) are now available as an R-package. You can download the package polspline from CRAN. (Version 1.0.11, 5/24/2005.)
• Software for logspline as well as the logspline version discussed in Stone et al (1997) are now available as an R-package. You can download the package logspline from CRAN. (Version 2,9,2, 4/18/2005.) The latest version of logspline is always part of the latest version of polspline.

A book about splines

• Statistical Modeling with Spline Functions, an unfinished, incomplete, monograph.