example

This is toy example of RNA-seq raw read count table. It containes 10000 genes  and 6 samples (three for case and other three for control group).

datasets

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.

Sora Yoon

AbsFilterGSEA

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

example function

A data frame with 10000 observations on the following 6 variables.
  <dl> </dl> 

Format

Cancer Genome Atlas Research, N. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013;499(7456):43-49.

example: Normalized RNA-seq count data

Description

Usage

Arguments

Format

Source

Details

References

Examples