bioc-issue-bot
commented
6 years ago Hi @zhushijia
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: GIGSEA
Type: Package
Title: Genotype Imputed Gene Set Enrichment Analysis
Version: 0.99.0
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: Matrix, MASS, locfdr, stats, utils
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
biocViews: GeneSetEnrichment,SNP,VariantAnnotation,GeneExpression,GeneRegulation,Regression,DifferentialExpression
LiNk-NY
zhushijia
lgeistlinger
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