annotatePeak : 'select()' returned 1:many mapping between keys and columns

[sunta3iouxos]

Hi all,

running ChiPseekeer, list<- as.list(c(narrow.peaks) peak=GenomicRanges::GRangesList(name=readPeakFile(list)) peak is a GRanges object created from narrowpeak file, taken from a MACS2 analysis. while peakAnnoList=lapply(peak, annotatePeak, TxDb = txdbhg19, annoDb = 'org.Hs.eg.db')I get the following: 'select()' returned 1:many mapping between keys and columns

what does it mean and should I ignore it, or should I check the narrow peak file? Thank you.

>> preparing features information...		 2020-05-12 09:31:44 
>> identifying nearest features...		 2020-05-12 09:31:44 
>> calculating distance from peak to TSS...	 2020-05-12 09:31:46 
>> assigning genomic annotation...		 2020-05-12 09:31:46 
>> adding gene annotation...			 2020-05-12 09:31:58 
'select()' returned 1:many mapping between keys and columns
>> assigning chromosome lengths			 2020-05-12 09:31:58 
>> done...					 2020-05-12 09:31:58 
>> preparing features information...		 2020-05-12 09:31:58 
>> identifying nearest features...		 2020-05-12 09:31:58 
>> calculating distance from peak to TSS...	 2020-05-12 09:31:59 
>> assigning genomic annotation...		 2020-05-12 09:31:59 
>> adding gene annotation...			 2020-05-12 09:32:01 
'select()' returned 1:many mapping between keys and columns
>> assigning chromosome lengths			 2020-05-12 09:32:02 
>> done...					 2020-05-12 09:32:02 
>> preparing features information...		 2020-05-12 09:32:02 
>> identifying nearest features...		 2020-05-12 09:32:02 
>> calculating distance from peak to TSS...	 2020-05-12 09:32:03 
>> assigning genomic annotation...		 2020-05-12 09:32:03 
>> adding gene annotation...			 2020-05-12 09:32:05 
'select()' returned 1:many mapping between keys and columns
>> assigning chromosome lengths			 2020-05-12 09:32:05 
>> done...					 2020-05-12 09:32:05 
>> preparing features information...		 2020-05-12 09:32:05 
>> identifying nearest features...		 2020-05-12 09:32:05 
>> calculating distance from peak to TSS...	 2020-05-12 09:32:06 
>> assigning genomic annotation...		 2020-05-12 09:32:06 
>> adding gene annotation...			 2020-05-12 09:32:08 
'select()' returned 1:many mapping between keys and columns
>> assigning chromosome lengths			 2020-05-12 09:32:08 
>> done...					 2020-05-12 09:32:08 

[sam-israel]

Not an official answer, but see here https://support.bioconductor.org/p/100899/