Gene Symbol Annotation
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@petermcerlean-9754
Last seen 5.2 years ago

Hi Lukas,

Is there anyway to annotate DERs with gene symbol as opposed to the ensemble ID? 

I've tried things like; annotation='HGNC-SYMBOL' or 'Symbol' both upper and lower case but don't seem to work. 

I can covert the IDs via biomart but this doesn't retain order or allow for multiple entries of the same ensemble ID.

Kind Regards,

Peter

medips • 701 views
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Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 3.7 years ago
USA/La Jolla/UCSD
Hi Peter, I think its not possible to annotate DERs with gene symbols using the MEDIPS.annotate function. I recommend to use other tools available in R/Bioconductor for annotating genomic coordinates, such as ChIPpeakAnno, I have no experience with it but I think it can do the job? All the best, Lukas On 18 Aug 2016, at 12:29, peter.mcerlean [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User peter.mcerlean<https: support.bioconductor.org="" u="" 9754=""/> wrote Question: Gene Symbol Annotation<https: support.bioconductor.org="" p="" 86288=""/>: Hi Lukas, Is there anyway to annotate DERs with gene symbol as opposed to the ensemble ID? I've tried things like; annotation='HGNC-SYMBOL' or 'Symbol' both upper and lower case but don't seem to work. I can covert the IDs via biomart but this doesn't retain order or allow for multiple entries of the same ensemble ID. Kind Regards, Peter ________________________________ Post tags: medips You may reply via email or visit Gene Symbol Annotation
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