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: | 1.5.1 |
Imports: | Rcpp, Biobase, stats, DESeq, limma |
LinkingTo: | Rcpp, RcppArmadillo |
Published: | 2017-09-21 |
Author: | Sora Yoon |
Maintainer: | Sora Yoon <yoonsora at unist.ac.kr> |
License: | GPL-2 |
NeedsCompilation: | yes |
CRAN checks: | AbsFilterGSEA results |
Reference manual: | AbsFilterGSEA.pdf |
Package source: | AbsFilterGSEA_1.5.1.tar.gz |
Windows binaries: | r-devel: AbsFilterGSEA_1.5.1.zip, r-release: AbsFilterGSEA_1.5.1.zip, r-oldrel: AbsFilterGSEA_1.5.1.zip |
OS X El Capitan binaries: | r-release: not available |
OS X Mavericks binaries: | r-oldrel: AbsFilterGSEA_1.5.1.tgz |
Old sources: | AbsFilterGSEA archive |
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