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license: LGPL-3.0-only
title: 'GIGSEA: Genotype Imputed Gene Set Enrichment Analysis'
version: 1.23.0
doi: 10.32614/CRAN.package.GIGSEA
abstract: 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.
authors:
- family-names: Zhu
  given-names: Shijia
  email: shijia.zhu@mssm.edu
repository: https://bioc.r-universe.dev
commit: 38b82ac570b74d335542eb5d7ee76aec6b9a7111
contact:
- family-names: Zhu
  given-names: Shijia
  email: shijia.zhu@mssm.edu