Package: GIGSEA
Type: Package
Title: Genotype Imputed Gene Set Enrichment Analysis
Version: 1.29.0
Author: Shijia Zhu
Maintainer: Shijia Zhu <shijia.zhu@mssm.edu>
Description: 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.
License: LGPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
biocViews:
        GeneSetEnrichment,SNP,VariantAnnotation,GeneExpression,GeneRegulation,Regression,DifferentialExpression
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:45:44 UTC
RemoteUrl: https://github.com/bioc/GIGSEA
RemoteRef: HEAD
RemoteSha: 456186a07a2bbc0bb935a1d465d771b1ebb5433f
Packaged: 2025-11-02 03:47:32 UTC; root
Built: R 4.6.0; ; 2025-11-02 03:48:56 UTC; windows
