GSEA {cinaR}

GSEA

Description

Gene set enrichment analyses, runs 'fgsea' package implementation with preset values.

Usage

GSEA(genes, geneset)

Arguments

genes

DA gene names to be checked if they are over-represented or not.

geneset

Pathways to be used in enrichment analyses. If not set vp2008 (Chaussabel, 2008) immune modules will be used. This can be set to any geneset using 'read.gmt' function from 'qusage' package. Different modules are available: https://www.gsea-msigdb.org/gsea/downloads.jsp.

Value

data.frame, list of pathways and their enrichment (adjusted) p-values.

References

G. Korotkevich, V. Sukhov, A. Sergushichev. Fast gene set enrichment analysis. bioRxiv (2019), doi:10.1101/060012

Examples

library(cinaR)
library(fgsea)
data(examplePathways)
data(exampleRanks)
GSEA(exampleRanks, examplePathways)