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

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.

Install the latest version of this package by entering the following in R:
install.packages("AbsFilterGSEA")
AuthorSora Yoon <yoonsora@unist.ac.kr>
Date of publication2016-08-26 20:35:18
MaintainerSora Yoon <yoonsora@unist.ac.kr>
LicenseGPL-2
Version1.5
http://rpubs.com/yoonsora/166897

View on CRAN

Files

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

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