clusterProfiler results problem

Question

[Gemini_Qiu]

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.

1. 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?
2. 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"

Answer 1

[Guangchuang Yu]

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.

[Gemini_Qiu]

Thanks, I got it now. Thanks for teaching patiently. I will submit with clusterprofiler next time, if I have another one.