Gene-Based Methods to Detect Gene-Gene Interaction in R: The GeneGeneInteR Package

IF 5.4 2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS
M. Emily, Nicolas Sounac, F. Kroell, Magalie Houée-Bigot
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引用次数: 3

Abstract

GeneGeneInteR is an R package dedicated to the detection of an association between a case-control phenotype and the interaction between two sets of biallelic markers (single nucleotide polymorphisms or SNPs) in case-control genome-wide associations studies. The development of statistical procedures for searching gene-gene interaction at the SNP-set level has indeed recently grown in popularity as these methods confer advantage in both statistical power and biological interpretation. However, all these methods have been implemented in home made softwares that are for most of them available only on request to the authors and at best have a web interface. Since the implementation of these methods is not straightforward, there is a need for a user-friendly tool to perform gene-based genegene interaction. The purpose of GeneGeneInteR is to propose a collection of tools for all the steps involved in gene-based gene-gene interaction testing in case-control association studies. Illustrated by an example of a dataset related to rheumatoid arthritis, this paper details the implementation of the functions available in GeneGeneInteR to perform an analysis of a collection of SNP sets. Such an analysis aims at addressing the complete statistical pipeline going from data importation to the visualization of the results through data manipulation and statistical analysis.
基于基因检测R基因-基因相互作用的方法:GeneGeneInteR包
GeneGeneInteR是一个R软件包,致力于在病例对照全基因组关联研究中检测病例对照表型与两组双等位基因标记(单核苷酸多态性或snp)之间的相互作用之间的关联。在snp集水平上搜索基因-基因相互作用的统计程序的发展最近确实越来越受欢迎,因为这些方法在统计能力和生物学解释方面都具有优势。然而,所有这些方法都是在国产软件中实现的,其中大多数只能根据作者的要求提供,充其量只有一个web界面。由于这些方法的实现并不简单,因此需要一种用户友好的工具来执行基于基因的基因相互作用。GeneGeneInteR的目的是为病例对照关联研究中基于基因的基因-基因相互作用测试的所有步骤提供一套工具。本文以类风湿关节炎相关数据集为例,详细介绍了GeneGeneInteR中可用功能的实现,以执行SNP集合的分析。这种分析旨在通过数据操作和统计分析解决从数据输入到结果可视化的完整统计管道。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Statistical Software
Journal of Statistical Software 工程技术-计算机:跨学科应用
CiteScore
10.70
自引率
1.70%
发文量
40
审稿时长
6-12 weeks
期刊介绍: The Journal of Statistical Software (JSS) publishes open-source software and corresponding reproducible articles discussing all aspects of the design, implementation, documentation, application, evaluation, comparison, maintainance and distribution of software dedicated to improvement of state-of-the-art in statistical computing in all areas of empirical research. Open-source code and articles are jointly reviewed and published in this journal and should be accessible to a broad community of practitioners, teachers, and researchers in the field of statistics.
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