clusterprofiler for comparing differentially expressed genes

Question

[najibveto]

hello, I am trying to compare the upregulated and downregulated genes in my non model organism. so I am trying to use the comparecluster function from clusterprofiler package. for that purpose I used the following code:

library("clusterProfiler")
library(ggplot2)
library(export)
library(cowplot)
setwd("D:/New folder/najib/Project05")
#load the down and up genes
gene <- read.csv("N402-DE-DOWN-UP-1.csv",header = T,sep=",",fileEncoding="UTF-8-BOM")
#load the GO and its associiated gene id
term2gene <- read.csv("N402-GO-gene.csv",header=T,sep=",")
#load the Go and their term 
term2name <- read.csv("N402-GO-term.csv",header=T,sep=",")
#use of comparcluster
X <- compareCluster (gene ,Fun ='enricher',TERM2GENE=term2gene,TERM2NAME=term2name,pvalueCutoff=0.1,pAdjustMethod="BH",qvalueCutoff=0.5)

however I got the following error:

> X <- compareCluster (gene ,Fun ='enricher',TERM2GENE=term2gene,TERM2NAME=term2name,pvalueCutoff=0.1,pAdjustMethod="BH",qvalueCutoff=0.5)
Error in fun(i, ...) : 
  unused arguments (Fun = "enricher", TERM2GENE = list(c("GO:0031177", "GO:0003824", "GO:0016627", "GO:0055114", "GO:0050660", "GO:0000049", "GO:0046872", "GO:0005524", "GO:0016491", "GO:0031177", "GO:0016740", "GO:0003824", "GO:0055114", "GO:0008270", "GO:0016491", "GO:0046872", "GO:0045454", "GO:0004252", "GO:0016021", "GO:0006355", "GO:0005634", "GO:0008270", "GO:0003700", "GO:0003676", "GO:0020037", "GO:0004497", "GO:0055114", "GO:0005506", "GO:0016712", "GO:0016705", "GO:0009439", "GO:0008824", "GO:0003677", 
"GO:0005634", "GO:0003676", "GO:0005515", "GO:0016020", "GO:0046873", "GO:0055085", "GO:0030001", "GO:0006887", "GO:0000145", "GO:0050032", "GO:0050660", "GO:0055114", "GO:0016491", "GO:0071949", "GO:0008410", "GO:0046952", "GO:0032543", "GO:0003735", "GO:0050661", "GO:0004499", "GO:0050660", "GO:0055114", "GO:0006383", "GO:0003677", "GO:0003899", "GO:0005666", "GO:0003824", "GO:0004065", "GO:0018958", "GO:0008484", "GO:0005634", "GO:0008270", "GO:0003677", "GO:0006351"

I uploaed the raw data at the following link: enter link description here

so what is the possible solution for this error?

thank you for help.

[andres.firrincieli]

unused arguments error: link

Carefully check the usage of compareCluster

[najibveto]

thank you for your answer, so the compareCluster is limited to : "groupGO", "enrichGO", "enrichKEGG", "enrichDO" or "enrichPathway" .

[andres.firrincieli]

I think the error is triggered by the argument Fun which should be fun

[najibveto]

thank you a lot. it is working fine now. really appreciate your help.