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
I would appreciate your help.