ClusterProfiler.GSEA: Perform GSEA analysis by cluster profiler
In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

ClusterProfiler.GSEA

R Documentation

Perform GSEA analysis by cluster profiler

Description

Perform GSEA analysis by cluster profiler

Usage

ClusterProfiler.GSEA(
  phenotype,
  geneNames,
  minGSSize = 10,
  qvalue = 0.05,
  GO = TRUE,
  KEGG = TRUE,
  MSigDb = TRUE,
  Hallmark = TRUE,
  exp.gene.type = "SYMBOL"
)

Arguments

`phenotype`	log2FC
`geneNames`	gene symbols. Must be symbol
`minGSSize`	10
`qvalue`	0.05
`GO`	TRUE
`KEGG`	TRUE
`MSigDb`	TRUE
`Hallmark`	TRUE
`exp.gene.type`	RNA expression ID ENSEMBL. keytypes(org.Hs.eg.db)