clusterProfiler: Input file format

Question

[Mike]

Hi All,

I'm using clusterProfiler but not able to run enrichGO on my datasets.

my Input data is like this:

gene entrez logFC P.Value q_value

ABR 29 -1.11808 0.01825 0.852004

ADAT3 113179 -0.0875548 0.9431 0.999156

AMDHD2 51005 -0.864244 0.3177 0.999156

ASNA1 439 -0.354129 0.53285 0.999156

ASPSCR1 79058 -0.255376 0.7536 0.999156

I want to use following commands:

library(clusterProfiler)

data(geneList)

gene <- names(geneList)[abs(geneList) > 2]

 ego <- enrichGO(gene= gene,universe= names(geneList),OrgDb= org.Hs.eg.db,ont= "CC",  pAdjustMethod = "BH", pvalueCutoff  = 0.01,qvalueCutoff  = 0.05, readable= TRUE)

cnetplot(ego, categorySize="pvalue", foldChange=geneList)

I went through clusterProfiler tutorial, but could not find about input file.

so how can I modify above code for my data.

Thanks,

Answer 1

[Jean-Karim Heriche]

Where is your problem ? Do you get any error ? The enrichGO() function takes as input a vector of Entrez gene IDs. So make sure that your gene variable is such a thing. Your code looks wrong. You probably want something like:

data<-read.delim("input.txt") # Assuming your file is tab-delimited
genes<-data$entrez[abs(data$logFC)>2]
ego<-enrichGO(gene=genes....)

EDIT: Use data$entrez to get the right column.

[Mike]

Thanks,

Im using same command, but got following errors

data<-read.delim("input.txt") 

genes<-data$gene[abs(data$logFC)>2]

 ego <- enrichGO(genes , organism= "human", ont= "CC",  pAdjustMethod = "BH", pvalueCutoff  = 0.1,qvalueCutoff  = 0.5, readable= TRUE)

 ego

[1] NA

also used

ego <- enrichGO(genes , organism= "human", ont= "CC",  pAdjustMethod = "BH", readable= TRUE)

ego

[1] NA

 cnetplot(ego, categorySize="pvalue", foldChange=genes)

Error in (function (classes, fdef, mtable)  : 

  unable to find an inherited method for function ‘cnetplot’ for signature ‘"logical"’

[Jean-Karim Heriche]

You need the Entrez gene IDs. I made a mistake in the code I wrote because the IDs are in data$entrez not in data$gene.

[Mike]

Thanks a lot, Jean-Karim Heriche,

it works now

[WouterDeCoster]

can you check whether your variable 'genes' is what you expect it to be by printing it?