clusterprofiler for comparing differentially expressed genes
0
0
Entering edit mode
6 days ago
najibveto ▴ 50

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.

clusterProfiler comparecluster • 196 views
ADD COMMENT
1
Entering edit mode

unused arguments error: link

Carefully check the usage of compareCluster

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1600 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6