Hi,
Recently,I want to do some pathway study, and found clusterProfiler updated, and used it.Now, I have some questions, appreciated if you do me a favor.
- I have 671 entrez id ,then annotated 278 according to "Count" column, I found that GeneRatio's denominator might be the input genes, which annotated with pathway. But the 278 (sum of numberator) and 288 (denominator) isn't equal, while I set the pvalueCutoff as 1.What is the exactly definition of GeneRatio's denominator? Am my understanding right?
- 671 input genes ,278 annotated? The other genes can't be annotated? Due to imcomplete gene discovery?
Thanks in advance!
Attached some codes:
my enrich code:
k<-enrichKEGG(gene=gene$V1,organism='osa',pvalueCutoff=1)
length(gene$V1)
#[1] 671
r<-summary(kk)
sum(r$Count)
#[1] 278
r$GeneRatio
# [1] "52/288" "13/288" "23/288" "21/288" "19/288" "35/288" "24/288" "14/288" "14/288" "12/288" "15/288"
#[12] "8/288" "5/288" "9/288" "7/288" "4/288" "3/288"
Online Test Code:
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]
tk<- enrichKEGG(gene= gene,organism= 'hsa',pvalueCutoff=1)
s<-summary(tk)
sum(s$Count)
#
#> sum(s$Count)
#[1] 56
#> s$GeneRatio
#[1] "11/84" "10/84" "7/84" "6/84" "5/84" "8/84" "9/84"
0. it would be better if you can tag your post with clusterprofiler, so that I can receive email notification.
1. only set pvalueCutoff=1 you still get a subset of the result. You need to also set qvalueCutoff=1.
> tk<- enrichKEGG(gene= gene,organism= 'hsa',pvalueCutoff=1, qvalueCutoff=1)
> sum(tk$Count)
[1] 349
> tk$GeneRatio[1]
[1] "11/84"
You can't just sum the Count column as 1 gene may belong to multiple pathways.
> geneInCategory(tk) %>% unlist %>% unique %>% length
[1] 84
2. It is quite common.
> head(tk, 2)
ID Description GeneRatio BgRatio pvalue p.adjust
hsa04110 hsa04110 Cell cycle 11/84 124/7173 1.685194e-07 2.949089e-05
hsa04114 hsa04114 Oocyte meiosis 10/84 124/7173 1.551940e-06 1.357948e-04
qvalue geneID Count
hsa04110 2.909177e-05 8318/991/9133/890/983/4085/7272/1111/891/4174/9232 11
hsa04114 1.339570e-04 991/9133/983/4085/51806/6790/891/9232/3708/5241 10
For human, there are only 7173 genes annotated by KEGG.
Thanks, I got it now. Thanks for teaching patiently. I will submit with clusterprofiler next time, if I have another one.
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