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Bioinformatics Advance Access originally published online on January 31, 2007
Bioinformatics 2007 23(5):654-655; doi:10.1093/bioinformatics/btm025
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SNPassoc: an R package to perform whole genome association studies

Juan R. González 1,*, Lluís Armengol 1, Xavier Solé 2, Elisabet Guinó 2, Josep M. Mercader 1, Xavier Estivill 1 and Víctor Moreno 2,*

1Genes and Disease Program, Centre for Genomic Regulation and 2Unit of Biostatistics and Bioinformatics, Epidemiology Service, IDIBELL, Catalan Institute of Oncology, Barcelona, Spain

*To whom correspondence should be addressed.


  Abstract

Summary: 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 the analysis of individual SNPs is a relatively trivial task, when the number is large and multiple genetic models need to be explored it becomes necessary a tool to automate the analyses. In order to address this issue, we developed SNPassoc, an R package to carry out most common analyses in 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).

Availability: Package SNPassoc is available at CRAN from http://cran.r-project.org

Contact: juanramon.gonzalez{at}crg.es or v.moreno{at}iconcologia.net

Supplementary information: A tutorial is available on Bioinformatics online and in http://davinci.crg.es/estivill_lab/snpassoc

Received on September 27, 2006; revised on January 22, 2007; accepted on January 22, 2007

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