GIGSEA
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GIGSEA.
Genotype Imputed Gene Set Enrichment Analysis
Bioconductor version: 3.9
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("GIGSEA")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneRegulation, GeneSetEnrichment, Regression, SNP, Software, VariantAnnotation |
| Version | 1.2.0 |
| 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 | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | GIGSEAdata |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GIGSEA_1.2.0.tar.gz |
| Windows Binary | GIGSEA_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | GIGSEA_1.2.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |