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Question: ChIPseeker mapping between keys and columns
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gravatar for rbronste
12 months ago by
rbronste60
rbronste60 wrote:

Wondering why I may be getting following semi-error:

 peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000),
+                          TxDb=TxDb.Mmusculus.UCSC.mm10.knownGene, annoDb="org.Mm.eg.db")
>> loading peak file...                 2017-09-27 15:51:35 
>> preparing features information...         2017-09-27 15:51:35 
>> identifying nearest features...         2017-09-27 15:51:35 
>> calculating distance from peak to TSS...     2017-09-27 15:51:36 
>> assigning genomic annotation...         2017-09-27 15:51:36 
>> adding gene annotation...             2017-09-27 15:51:48 
'select()' returned 1:many mapping between keys and columns
>> assigning chromosome lengths             2017-09-27 15:51:48 
>> done...                     2017-09-27 15:51:48 ​
ADD COMMENTlink modified 12 months ago by Gavin Kelly560 • written 12 months ago by rbronste60
2
gravatar for Gavin Kelly
12 months ago by
Gavin Kelly560
United Kingdom / London / Francis Crick Institute
Gavin Kelly560 wrote:

The "1:many" is referring to the fact that there are multiple entries in the org.Mm.eg.db annotation that have the same Entrez-gene id, so alternative gene names or symbols. It looks like chipseeker deals with this by selecting the first one that is found, so it's nothing to worry about, except you may not recognise certain synonyms for familiar genes.

ADD COMMENTlink written 12 months ago by Gavin Kelly560
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