Question: ChIPseeker mapping between keys and columns
0
gravatar for rbronste
2.2 years 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 ​
chipseq chipseeker • 531 views
ADD COMMENTlink modified 2.2 years ago by Gavin Kelly570 • written 2.2 years ago by rbronste60
Answer: ChIPseeker mapping between keys and columns
2
gravatar for Gavin Kelly
2.2 years ago by
Gavin Kelly570
United Kingdom / London / Francis Crick Institute
Gavin Kelly570 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 2.2 years ago by Gavin Kelly570
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