GIGSEA

DOI: 10.18129/B9.bioc.GIGSEA    

Genotype Imputed Gene Set Enrichment Analysis

Bioconductor version: Release (3.13)

We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal.

Author: Shijia Zhu

Maintainer: Shijia Zhu <shijia.zhu at mssm.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GIGSEA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GIGSEA")

 

PDF	R Script	GIGSEA: Genotype Imputed Gene Set Enrichment Analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneRegulation, GeneSetEnrichment, Regression, SNP, Software, VariantAnnotation
Version	1.10.0
In Bioconductor since	BioC 3.8 (R-3.5) (3 years)
License	LGPL-3
Depends	R (>= 3.5), Matrix, MASS, locfdr, stats, utils
Imports
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	GIGSEAdata
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GIGSEA_1.10.0.tar.gz
Windows Binary	GIGSEA_1.10.0.zip
macOS 10.13 (High Sierra)	GIGSEA_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GIGSEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GIGSEA
Package Short Url	https://bioconductor.org/packages/GIGSEA/
Package Downloads Report	Download Stats