ChIPseeker mapping between keys and columns
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rbronste ▴ 60
@rbronste-12189
Last seen 23 months ago

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 ​
chipseeker chipseq • 798 views
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Gavin Kelly ▴ 590
@gavin-kelly-6944
Last seen 18 months ago
United Kingdom / London / Francis Crick…

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.

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