SNPassoc

An R package to perform whole genome association studies

Juan Ramon González, Lluís Armengol, Xavier Solé, Elisabet Guinó, Josep M. Mercader, Xavier P. Estivill, Víctor Moreno

Research output: Contribution to journalArticle

462 Citations (Scopus)

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).

Original languageEnglish
Pages (from-to)644-645
Number of pages2
JournalBioinformatics
Volume23
Issue number5
DOIs
Publication statusPublished - Mar 2007
Externally publishedYes

Fingerprint

Single nucleotide Polymorphism
Genome-Wide Association Study
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Genome
Genes
Equilibrium Analysis
Epistasis
Genetic Association
Exploratory Analysis
Haplotype
Genetic Models
Missing Values
Genetic Association Studies
Generalized Linear Model
Susceptibility
Haplotypes
Linear Models
Trivial

ASJC Scopus subject areas

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

González, J. R., Armengol, L., Solé, X., Guinó, E., Mercader, J. M., Estivill, X. P., & Moreno, V. (2007). SNPassoc: An R package to perform whole genome association studies. Bioinformatics, 23(5), 644-645. https://doi.org/10.1093/bioinformatics/btm025

SNPassoc : An R package to perform whole genome association studies. / González, Juan Ramon; Armengol, Lluís; Solé, Xavier; Guinó, Elisabet; Mercader, Josep M.; Estivill, Xavier P.; Moreno, Víctor.

In: Bioinformatics, Vol. 23, No. 5, 03.2007, p. 644-645.

Research output: Contribution to journalArticle

González, JR, Armengol, L, Solé, X, Guinó, E, Mercader, JM, Estivill, XP & Moreno, V 2007, 'SNPassoc: An R package to perform whole genome association studies', Bioinformatics, vol. 23, no. 5, pp. 644-645. https://doi.org/10.1093/bioinformatics/btm025
González JR, Armengol L, Solé X, Guinó E, Mercader JM, Estivill XP et al. SNPassoc: An R package to perform whole genome association studies. Bioinformatics. 2007 Mar;23(5):644-645. https://doi.org/10.1093/bioinformatics/btm025
González, Juan Ramon ; Armengol, Lluís ; Solé, Xavier ; Guinó, Elisabet ; Mercader, Josep M. ; Estivill, Xavier P. ; Moreno, Víctor. / SNPassoc : An R package to perform whole genome association studies. In: Bioinformatics. 2007 ; Vol. 23, No. 5. pp. 644-645.
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