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.

Version: 1.5
Depends: R (≥ 3.3.1)
Imports: Rcpp, limma, DESeq
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat
Published: 2016-08-26
Author: Sora Yoon
Maintainer: Sora Yoon <yoonsora at unist.ac.kr>
License: GPL-2
URL: http://rpubs.com/yoonsora/166897
NeedsCompilation: yes
CRAN checks: AbsFilterGSEA results

Downloads:

Reference manual: AbsFilterGSEA.pdf
Package source: AbsFilterGSEA_1.5.tar.gz
Windows binaries: r-devel: AbsFilterGSEA_1.5.zip, r-release: AbsFilterGSEA_1.5.zip, r-oldrel: AbsFilterGSEA_1.5.zip
OS X El Capitan binaries: r-release: not available
OS X Mavericks binaries: r-oldrel: AbsFilterGSEA_1.5.tgz
Old sources: AbsFilterGSEA archive

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