SNPs-Based Whole Genome Association Studies

Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al. (2007) .


Reference manual

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2.0-2 by Juan R Gonzalez, a year ago

Browse source code at

Authors: Juan R Gonzalez and Victor Moreno

Documentation:   PDF Manual  

Task views: Statistical Genetics, Missing Data

GPL (>= 2) license

Imports haplo.stats, mvtnorm, parallel, survival, tidyr, plyr, ggplot2, BiocStyle, poisbinom

Suggests testthat, knitr, rmarkdown, biomaRt

See at CRAN