GSEA {cinaR} | R Documentation |
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)
[Package cinaR version 0.2.3 Index]