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annotatePeak : 'select()' returned 1:many mapping between keys and columns
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
Not an official answer, but see here https://support.bioconductor.org/p/100899/