clusterprofile enrichment analysis

Hello, Can I use clusterprofile enrichment functions like enrichGO() in case I have ensemblId and symbol(gene name) from old version GTF file (as they will not mapped or join with org.Hs.eg.db ). and which database can be passed for OrgDb param in enrich GO other that org.Hs.eg.db

Thanks

enrichment analysis clusterprofile

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updated 3.2 years ago by mark.ziemann

• written 3.2 years ago by ahmad •

1 answer

If you have your own GTF file of gene sets, the function to use is enricher()

EDIT Sorry I didn't read your question properly the first time. Easiest solution for you is to convert the Ensembl IDs to entrez IDs. There is code for this here: Ensembl ID to ENTREZ best converter

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written 3.2 years ago by mark.ziemann

Thank you for replaying. I have GTF file that I have use for alignment process ,the following one: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_24/

So I do no think that it has information about ontology terms !!!

thank you again

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written 3.2 years ago by ahmad •

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