Gonzalez JR, Armengol L, Sole X, Guino E, Mercader JM, Estivill X, Moreno V.
Aim: The popularization of large scale genotyping projects has led to the widespread adoption of genetic association studies as the tool of choice in the search for single nucleotide polymorphisms (SNPs) underlying susceptibility to complex diseases. Although analysis of individual SNPs is a relatively trivial task to conduct, the large amount of possible combinations of SNPs, diseases and association models to be explored makes it necessary to have an automated tool to perform these analyses routinely.
Description: The R package SNPassoc contains classes and methods to help the analysis of whole genome association studies. SNPassoc utilizes S4 classes and extends haplo.stats R package to facilitate haplotype analyses. The package is useful to carry out most common analysis when performing whole genome association studies. 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.