ChIPseeker mapping between keys and columns
1
0
Entering edit mode
rbronste ▴ 60
@rbronste-12189
Last seen 4.3 years 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 • 2.4k views
ADD COMMENT
2
Entering edit mode
Gavin Kelly ▴ 680
@gavin-kelly-6944
Last seen 3.9 years 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.

ADD COMMENT

Login before adding your answer.

Traffic: 788 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6