Gene-Based Methods to Detect Gene-Gene Interaction in R: The GeneGeneInteR Package
Dublin Core
Title
Gene-Based Methods to Detect Gene-Gene Interaction in R: The GeneGeneInteR Package
Subject
association studies, gene-gene interaction, dependence, single nucleotide polymophism
Description
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
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
Creator
Mathieu Emily
Source
https://www.jstatsoft.org/article/view/v095i12
Publisher
Agrocampus Ouest
IRMAR UMR 6625
IRMAR UMR 6625
Date
October 2020
Contributor
Fajar bagus W
Format
PDF
Language
Inggris
Type
Text
Files
Collection
Citation
Mathieu Emily, “Gene-Based Methods to Detect Gene-Gene Interaction in R: The GeneGeneInteR Package,” Repository Horizon University Indonesia, accessed April 11, 2025, https://repository.horizon.ac.id/items/show/8162.