enrichKEGG function error
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@d4a334e3
Last seen 10 months ago
Germany

Hello, I was trying to check kegg enrichment analysis for my Bulk RNAseq DGE results, and I am getting this error --> No gene can be mapped.... --> Expected input gene ID:
--> return NULL... could you kindly tell what might be gone wrong?

input: KeggSegGen <- shrink.tab %>% drop_na(Entrez,FDR) %>% dplyr:: filter(FDR < 0.05)%>% pull(Entrez)

head(KeggSegGen)

KeggRes <- enrichKEGG(gene = KeggSegGen, organism = 'mmu')

output: [1] 67608 12390 23849 29871 12858 22415

--> No gene can be mapped.... --> Expected input gene ID:
--> return NULL...

thank you in advance!
cluster clusterProfiler KEGG • 2.0k views
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Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

Double-check that your input KeggSegGen is a character vector.

In case you did not do so yet; checking the help page of the function (by typing ?enrichKEGG) may also be helpful. You can check the example code, and confirm that your input structures are the same.
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thank you for your reply and help it was integer vector actually, I changed it into character, but still got the same results unfortunately. is there anything else I might have missed?

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In my hands it is working... See below. So I believe it must have something to do with the type of input you use.

When using the 6 ids you listed in your first post:

> library(clusterProfiler)
> 
> KeggSegGen <- c("67608","12390","23849","29871","12858","22415")
> 
> class(KeggSegGen)
[1] "character"
> 
> str(KeggSegGen)
 chr [1:6] "67608" "12390" "23849" "29871" "12858" "22415"
> 
> KeggRes <- enrichKEGG(gene = KeggSegGen, organism = 'mmu', pvalueCutoff=1)
> 
> KeggRes
#
# over-representation test
#
#...@organism    mmu 
#...@ontology    KEGG 
#...@keytype     kegg 
#...@gene        chr [1:6] "67608" "12390" "23849" "29871" "12858" "22415"
#...pvalues adjusted by 'BH' with cutoff <1 
#...29 enriched terms found
'data.frame':   29 obs. of  9 variables:
 $ ID         : chr  "mmu05205" "mmu05020" "mmu05010" "mmu05022" ...
 $ Description: chr  "Proteoglycans in cancer - Mus musculus (house mouse)" "Prion disease - Mus musculus (house mouse)" "Alzheimer disease - Mus musculus (house mouse)" "Pathways of neurodegeneration - multiple diseases - Mus musculus (house mouse)" ...
 $ GeneRatio  : chr  "2/3" "2/3" "2/3" "2/3" ...
 $ BgRatio    : chr  "205/9175" "268/9175" "383/9175" "471/9175" ...
 $ pvalue     : num  0.00147 0.0025 0.00507 0.00762 0.02046 ...
 $ p.adjust   : num  0.0363 0.0363 0.049 0.0553 0.0852 ...
 $ qvalue     : num  0.0211 0.0211 0.0285 0.0321 0.0495 ...
 $ geneID     : chr  "12390/22415" "12390/12858" "12858/22415" "12858/22415" ...
 $ Count      : int  2 2 2 2 1 1 1 1 1 1 ...
#...Citation
 T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.
 clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.
 The Innovation. 2021, 2(3):100141 

>
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yeah it's super weird, also when I change the function to enrichMKEGG it works normally, only using enrichKEGG doesn't work :/

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I have found out that r and all packages together should be updated and the same code went smoothly as normal.

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