cinaR (version 0.2.3)

GSEA: 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

# NOT RUN {
library(cinaR)
library(fgsea)
data(examplePathways)
data(exampleRanks)
GSEA(exampleRanks, examplePathways)
# }