SNPassoc: an R package to perform whole genome association studies
Open Access
- 31 January 2007
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 23 (5), 654-655
- https://doi.org/10.1093/bioinformatics/btm025
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@crg.es or v.moreno@iconcologia.net Supplementary information: A tutorial is available on Bioinformatics online and in http://davinci.crg.es/estivill_lab/snpassocKeywords
This publication has 3 references indexed in Scilit:
- SNPStats: a web tool for the analysis of association studiesBioinformatics, 2006
- A Note on Exact Tests of Hardy-Weinberg EquilibriumAmerican Journal of Human Genetics, 2005
- Genome-wide association studies for common diseases and complex traitsNature Reviews Genetics, 2005