enrichGO: Parameter "universe" and library "org.At.tair.db"

[Guerande29]

Hi, I do overrepresentation analysis for Arabidopsis. If I use the "org.At.tair.db" library,. My question: it is mandatory to use the "universe" file? or can I run the analysis without this parameter? Thank you

library(clusterProfiler) library(org.At.tair.db) library(forcats) library(enrichplot) library(pathview) library(data.table) library(ggplot2) library(GOsummaries) library(DOSE)

######### Over-Representation Analysis (ORA) with ClusterProfiler setwd("D:/M/Clusterprofiler")

Universe universe<- read.delim ("At11_universe.txt") universe<-as.character(universe[,1]) universe <- sort(universe, decreasing = TRUE)

DEGs Upregulated DEG_Upgrupos = read.delim("ComparisonUP.txt", header = TRUE) gene<-as.character(DEG_Upgrupos[,1]) gene <- sort(gene, decreasing = TRUE)

ORA

funtion enricGO # only BP

##pAdjustMethod: BH: Benjamini-Hochberg multiple testing procedure. Performs the Benjamini-Hochberg FDR-controlling method for multiple hypothesis testing. ORA_Upgrupos <- compareCluster(geneClusters=DEG_Upgrupos,enrichGO, OrgDb = org.At.tair.db, keyType = "TAIR", ont = "BP", universe = universe, pAdjustMethod = "BH", pvalueCutoff = 0.05, qvalueCutoff = 0.05)