Package: AbsFilterGSEA
Type: Package
Title: Improved False Positive Control of Gene-Permuting GSEA with
        Absolute Filtering
Version: 1.5.1
Author: Sora Yoon <yoonsora@unist.ac.kr>
Maintainer: Sora Yoon <yoonsora@unist.ac.kr>
Description: 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.
License: GPL-2
LazyData: TRUE
RoxygenNote: 6.0.1
Depends:
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, Biobase, stats, DESeq, limma
NeedsCompilation: yes
Packaged: 2017-09-21 13:27:08 UTC; ysora
Repository: CRAN
Date/Publication: 2017-09-21 13:39:52 UTC
Built: R 4.0.2; x86_64-w64-mingw32; 2020-08-02 09:37:46 UTC; windows
Archs: i386, x64
