Hello everyone! I am trying to annotate a list of regions as my regions are 502 bp long sometimes they overlap with more than 2 distinct genes , for example chr2:112541661_112542162 overlaps with both POLR1B and LOC105373562 ( the first gene is on + strand and the latter is on - strand). I am using annotatePeak function as follows:

txdb<- TxDb.Hsapiens.UCSC.hg38.knownGene
G.coor<- as_granges(coor , seqnames=seqnames , start=start , end=end)
annotation<- annotatePeak(G.coor , TxDb = txdb ,level = "gene"  , addFlankGeneInfo=TRUE )

and this message appears

>> preparing features information...         2021-07-12 16:38:13 
  1613 genes were dropped because they have exons located on both strands of the same reference sequence or on more
  than one reference sequence, so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to
  suppress this message.
>> identifying nearest features...       2021-07-12 16:38:15 
>> calculating distance from peak to TSS...  2021-07-12 16:38:16 
>> assigning genomic annotation...       2021-07-12 16:38:16 
>> adding flank feature information from peaks...    2021-07-12 16:38:48 
>> assigning chromosome lengths          2021-07-12 16:38:49 
>> done...                   2021-07-12 16:38:49 

for my example (chr2:112541661_112542162 ) this only shows POLR1B gene for annotation. how can I get annotations for all genes that overlap with my list of regions ?

also I'm not sure how to set 'single.strand.genes.only=FALSE' as it is not a parameter of annotatePeak

I would appreciate your help.

When using the TxDb.Hsapiens.UCSC.hg38.knownGene package, annotatePeak will just do

features <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene)

And you will see the message about the genes being dropped. Unfortunately the help page for this function is less than helpful, as it says

Arguments:

    peak: peak file or GRanges object

tssRegion: Region Range of TSS

    TxDb: TxDb or EnsDb annotation object

Which is not entirely correct. You can also pass in a GRanges object as the TxDb argument. So simply doing

TxDb <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene, single.strand.genes.only = FALSE)
annotation<- annotatePeak(G.coor , TxDb = TxDb ,level = "gene"  , addFlankGeneInfo=TRUE )

should get you where you want to go.