SNPassoc:: an R package to perform whole genome association studies
SNPassoc:: an R package to perform whole genome association studies
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DOI：
10.1093/bioinformatics/btm025
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发表时间：
2007-03-01
期刊：
影响因子：
5.8
通讯作者：
Moreno, Victor
中科院分区：
文献类型：
--
作者：
Gonzalez, Juan R.;Armengol, Lluis;Moreno, Victor
大规模基因分型项目的普及导致了遗传关联研究的广泛采用，作为寻找复杂疾病易感性的单核苷酸多态(SNPs)的首选工具。虽然对单个SNPs的分析是一项相对微不足道的任务，但当数量很大，需要探索多种遗传模型时，它就成为自动化分析的必要工具。为了解决这个问题，我们开发了SNPassoc，这是一个R包，用于在全基因组关联研究中进行最常见的分析。这些分析包括对缺失值的描述性统计和探索性分析，哈代-温伯格平衡的计算，基于广义线性模型的关联分析(对于数量性状或二元性状)，以及对多个SNP的分析(单倍型和上位性分析)。可用性：SNPassoc包可在CRAN上从http://cran.r-project.orgContact：juanramon.Gonzalez@crg.es或v.moreno@iconcolgia.net获得。补充信息：在线和http://davinci.crg.es/estivill_lab/snpassoc.上提供生物信息学教程
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.orgContact: juanramon.gonzalez@crg.es or v.moreno@iconcologia.netSupplementary information: A tutorial is available on Bioinformatics online and in http://davinci.crg.es/estivill_lab/snpassoc.