GIGSEA

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see GIGSEA.

Genotype Imputed Gene Set Enrichment Analysis


Bioconductor version: 3.18

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>

Citation (from within R, enter citation("GIGSEA")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
GIGSEA: Genotype Imputed Gene Set Enrichment Analysis PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GeneRegulation, GeneSetEnrichment, Regression, SNP, Software, VariantAnnotation
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License LGPL-3
Depends R (>= 3.5), Matrix, MASS, locfdr, stats, utils
Imports
System Requirements
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Suggests knitr, rmarkdown
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Depends On Me
Imports Me
Suggests Me GIGSEAdata
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Package Archives

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

Source Package GIGSEA_1.20.0.tar.gz
Windows Binary GIGSEA_1.20.0.zip
macOS Binary (x86_64) GIGSEA_1.20.0.tgz
macOS Binary (arm64) GIGSEA_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GIGSEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GIGSEA
Bioc Package Browser https://code.bioconductor.org/browse/GIGSEA/
Package Short Url https://bioconductor.org/packages/GIGSEA/
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