YuLab-SMU
Why doesn’t enrichKEGG() support the readable = TRUE parameter like enrichGO()?
The function enrichKEGG() does not seem to support the readable = TRUE/FALSE parameter, unlike enrichGO(). However, the resulting S4 object returned by enrichKEGG() still contains a logical slot named "readable".
Is this an intentional design choice, or is there a way to enable gene ID to gene symbol conversion in enrichKEGG() results, similar to what enrichGO(readable = TRUE) provides?
Yes, that is correct. I don't know whether Guangchuang did this intentionally, or not.
Anyway, applying the function setReadable() to the results obtained through enrichKEGG() will do this conversion as well. The readable 'slot' will then also be set to TRUE.
> library(clusterProfiler)
>
> data(geneList, package='DOSE')
> de <- names(geneList)[1:200]
>
> xx <- enrichKEGG(de, pvalueCutoff=0.01)
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> head(xx)
category
hsa04110 Cellular Processes
hsa04657 Organismal Systems
hsa04218 Cellular Processes
hsa04061 Environmental Information Processing
hsa04114 Cellular Processes
hsa04914 Organismal Systems
subcategory ID
hsa04110 Cell growth and death hsa04110
hsa04657 Immune system hsa04657
hsa04218 Cell growth and death hsa04218
hsa04061 Signaling molecules and interaction hsa04061
hsa04114 Cell growth and death hsa04114
hsa04914 Endocrine system hsa04914
Description
hsa04110 Cell cycle
hsa04657 IL-17 signaling pathway
hsa04218 Cellular senescence
hsa04061 Viral protein interaction with cytokine and cytokine receptor
hsa04114 Oocyte meiosis
hsa04914 Progesterone-mediated oocyte maturation
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
hsa04110 21/113 158/9434 0.13291139 11.096337 14.091100 1.240312e-16
hsa04657 10/113 95/9434 0.10526316 8.788076 8.399911 1.752488e-07
hsa04218 11/113 157/9434 0.07006369 5.849388 6.746304 2.577890e-06
hsa04061 9/113 100/9434 0.09000000 7.513805 7.209975 2.819340e-06
hsa04114 10/113 139/9434 0.07194245 6.006239 6.546772 5.952070e-06
hsa04914 8/113 111/9434 0.07207207 6.017061 5.854178 5.235706e-05
p.adjust qvalue
hsa04110 2.356593e-14 2.167282e-14
hsa04657 1.664863e-05 1.531121e-05
hsa04218 1.339186e-04 1.231606e-04
hsa04061 1.339186e-04 1.231606e-04
hsa04114 2.261787e-04 2.080092e-04
hsa04914 1.657974e-03 1.524785e-03
geneID
hsa04110 8318/991/9133/10403/890/983/4085/81620/7272/9212/1111/9319/891/4174/9232/4171/993/990/5347/701/9700
hsa04657 4312/6280/6279/6278/3627/2921/6364/8061/4318/3576
hsa04218 2305/4605/9133/890/983/51806/1111/891/993/3576/1978
hsa04061 3627/10563/6373/4283/6362/6355/2921/6364/3576
hsa04114 991/9133/983/4085/51806/6790/891/9232/5347/9700
hsa04914 9133/890/983/4085/6790/891/993/5347
Count
hsa04110 21
hsa04657 10
hsa04218 11
hsa04061 9
hsa04114 10
hsa04914 8
>
> yy <- setReadable(xx, OrgDb='org.Hs.eg.db', keyType='ENTREZID')
> head(yy)
category
hsa04110 Cellular Processes
hsa04657 Organismal Systems
hsa04218 Cellular Processes
hsa04061 Environmental Information Processing
hsa04114 Cellular Processes
hsa04914 Organismal Systems
subcategory ID
hsa04110 Cell growth and death hsa04110
hsa04657 Immune system hsa04657
hsa04218 Cell growth and death hsa04218
hsa04061 Signaling molecules and interaction hsa04061
hsa04114 Cell growth and death hsa04114
hsa04914 Endocrine system hsa04914
Description
hsa04110 Cell cycle
hsa04657 IL-17 signaling pathway
hsa04218 Cellular senescence
hsa04061 Viral protein interaction with cytokine and cytokine receptor
hsa04114 Oocyte meiosis
hsa04914 Progesterone-mediated oocyte maturation
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
hsa04110 21/113 158/9434 0.13291139 11.096337 14.091100 1.240312e-16
hsa04657 10/113 95/9434 0.10526316 8.788076 8.399911 1.752488e-07
hsa04218 11/113 157/9434 0.07006369 5.849388 6.746304 2.577890e-06
hsa04061 9/113 100/9434 0.09000000 7.513805 7.209975 2.819340e-06
hsa04114 10/113 139/9434 0.07194245 6.006239 6.546772 5.952070e-06
hsa04914 8/113 111/9434 0.07207207 6.017061 5.854178 5.235706e-05
p.adjust qvalue
hsa04110 2.356593e-14 2.167282e-14
hsa04657 1.664863e-05 1.531121e-05
hsa04218 1.339186e-04 1.231606e-04
hsa04061 1.339186e-04 1.231606e-04
hsa04114 2.261787e-04 2.080092e-04
hsa04914 1.657974e-03 1.524785e-03
geneID
hsa04110 CDC45/CDC20/CCNB2/NDC80/CCNA2/CDK1/MAD2L1/CDT1/TTK/AURKB/CHEK1/TRIP13/CCNB1/MCM5/PTTG1/MCM2/CDC25A/CDC6/PLK1/BUB1B/ESPL1
hsa04657 MMP1/S100A9/S100A8/S100A7/CXCL10/CXCL3/CCL20/FOSL1/MMP9/CXCL8
hsa04218 FOXM1/MYBL2/CCNB2/CCNA2/CDK1/CALML5/CHEK1/CCNB1/CDC25A/CXCL8/EIF4EBP1
hsa04061 CXCL10/CXCL13/CXCL11/CXCL9/CCL18/CCL8/CXCL3/CCL20/CXCL8
hsa04114 CDC20/CCNB2/CDK1/MAD2L1/CALML5/AURKA/CCNB1/PTTG1/PLK1/ESPL1
hsa04914 CCNB2/CCNA2/CDK1/MAD2L1/AURKA/CCNB1/CDC25A/PLK1
Count
hsa04110 21
hsa04657 10
hsa04218 11
hsa04061 9
hsa04114 10
hsa04914 8
>
>
Thanks for your response! Yes, I'm aware of the setReadable() function and have used it before — it works well.
I was just curious why enrichKEGG() doesn't support the readable parameter directly, like enrichGO() does. I'm wondering whether this is a design decision or just hasn't been implemented yet.