fgsea: Wrapper to run methods for preranked gene set enrichment...

In fgsea: Fast Gene Set Enrichment Analysis

Description

This function provide an interface to two existing functions: fgseaSimple, fgseaMultilevel. By default, the fgseaMultilevel function is used for analysis. For compatibility with the previous implementation you can pass the 'nperm' argument to the function.

Usage

fgsea(...)

Arguments

...	optional arguments for functions fgseaSimple, fgseaMultilevel

Value

A table with GSEA results. Each row corresponds to a tested pathway.

Examples

data(examplePathways)
data(exampleRanks)
fgseaRes <- fgsea(examplePathways, exampleRanks, maxSize=500)
# Testing only one pathway is implemented in a more efficient manner
fgseaRes1 <- fgsea(examplePathways[1], exampleRanks)

Example output

Warning message:
In fgseaMultilevel(...) :
  For some pathways, in reality P-values are less than 1e-10. You can set the `eps` argument to zero for better estimation.

fgsea documentation built on Nov. 8, 2020, 5:22 p.m.