I have some questions on what exactly is stored in the resulting KEGG.db, and how that relates to the options of clusterProfiler::enrichKEGG.
enrichKEGG has an option keyType, which accepts kegg, ncbi-geneid, ncbi-proteinid or uniprot.
Background/context
I would like to have a solution for doing KEGG enrichment analysis, starting from gene SYMBOL. I want to be able to use the same solution from any arbitrary species.
A rule of thumb for the ‘kegg’ ID is entrezgene ID for eukaryote species and Locus ID for prokaryotes.
I conclude that kegg id are not reliable enough/not sufficiently well described for my use. I would thus prefer to use ncbi-geneid.
However, when opening the sqlite database created through createKEGGdb, I only see a field gene_or_orf_id in table pathway2gene.
Questions:
what is the gene_or_orf_id present in the KEGG.db database? Is it a kegg id?
can I use createKEGGdb to create a KEGG.db package, and then use it for clusterProfiler::enrichKEGG with keyType = ncbi-geneid (and use_internal_data = TRUE)
Hello,
Thanks for this useful package!
I have some questions on what exactly is stored in the resulting
KEGG.db
, and how that relates to the options ofclusterProfiler::enrichKEGG
.enrichKEGG
has an optionkeyType
, which acceptskegg
,ncbi-geneid
,ncbi-proteinid
oruniprot
.Background/context
I would like to have a solution for doing KEGG enrichment analysis, starting from gene SYMBOL. I want to be able to use the same solution from any arbitrary species.
From this reply https://github.com/YuLab-SMU/clusterProfiler/issues/108#issuecomment-336784558
and this blog post https://guangchuangyu.github.io/2016/05/convert-biological-id-with-kegg-api-using-clusterprofiler/
I conclude that
kegg
id are not reliable enough/not sufficiently well described for my use. I would thus prefer to usencbi-geneid
.However, when opening the
sqlite
database created throughcreateKEGGdb
, I only see a fieldgene_or_orf_id
in tablepathway2gene
.Questions:
gene_or_orf_id
present in theKEGG.db
database? Is it akegg
id?createKEGGdb
to create aKEGG.db
package, and then use it forclusterProfiler::enrichKEGG
withkeyType = ncbi-geneid
(anduse_internal_data = TRUE
)Than you in advance for your help, All the best