AbsFilterGSEA: Improved False Positive Control of Gene-Permuting GSEA with Absolute Filtering

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Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.

Author
Sora Yoon <yoonsora@unist.ac.kr>
Date of publication
2016-08-26 20:35:18
Maintainer
Sora Yoon <yoonsora@unist.ac.kr>
License
GPL-2
Version
1.5
URLs

View on CRAN

Man pages

example
Normalized RNA-seq count data
GenePermGSEA
Gene permuting GSEA with or without filtering by absolute...

Files in this package

AbsFilterGSEA
AbsFilterGSEA/src
AbsFilterGSEA/src/AbsFilterGSEA.cpp
AbsFilterGSEA/src/RcppExports.cpp
AbsFilterGSEA/NAMESPACE
AbsFilterGSEA/data
AbsFilterGSEA/data/example.rda
AbsFilterGSEA/R
AbsFilterGSEA/R/GenePermGSEA.R
AbsFilterGSEA/R/RcppExports.R
AbsFilterGSEA/MD5
AbsFilterGSEA/DESCRIPTION
AbsFilterGSEA/man
AbsFilterGSEA/man/GenePermGSEA.Rd
AbsFilterGSEA/man/example.Rd