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.

Documentation

Manual: AbsFilterGSEA.pdf
Vignette: None available.

Maintainer: Sora Yoon <yoonsora at unist.ac.kr>

Author(s): Sora Yoon <yoonsora at unist.ac.kr>

Install package and any missing dependencies by running this line in your R console:

install.packages("AbsFilterGSEA")

Depends R (>= 3.3.1)
Imports Rcpp, limma, DESeq
Suggests testthat
Enhances
Linking to Rcpp, RcppArmadillo
Reverse
depends
Reverse
imports
Reverse
suggests
Reverse
enhances
Reverse
linking to

Package AbsFilterGSEA
Materials
URL http://rpubs.com/yoonsora/166897
Task Views
Version 1.5
Published 2016-08-26
License GPL-2
BugReports
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks AbsFilterGSEA check results
Package source AbsFilterGSEA_1.5.tar.gz