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Bioinformatics. 2007 Mar 1;23(5):644-5. Epub 2007 Jan 31.

SNPassoc: an R package to perform whole genome association studies.

Author information

  • 1Genes and Disease Program, Centre for Genomic Regulation, IDIBELL, Catalan Institute of Oncology, Barcelona, Spain. juanramon.gonzalez@crg.es

Abstract

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.

SUPPLEMENTARY INFORMATION:

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

PMID:
17267436
DOI:
10.1093/bioinformatics/btm025
[PubMed - indexed for MEDLINE]
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