I have done the differential accessibility analysis then annotated the region with chipseeker.
my output for one of the many region and question regarding this
Peak log2FoldChange padj seqnames start end width strand annotation geneChr geneStart 105 Peak32946 -1.992474 9.197721e-19 chr11 14078815 14079558 744 * Distal Intergenic 11 13962689 5445 Peak32938 -2.473959 4.878995e-04 chr11 13961467 13961818 352 * Promoter 11 13962689 geneEnd geneLength geneStrand geneId transcriptId distanceToTSS ENSEMBL SYMBOL GENENAME 105 14267884 305196 1 10418 ENST00000576479.3 116126 ENSG00000262655 SPON1 spondin 1 5445 14267884 305196 1 10418 ENST00000576479.3 -871 ENSG00000262655 SPON1 spondin 1
So the same region is marked as Distal Intergenic and Promoter. Next I have the same comparison RNA seq expression data. So now my objective is to find those genes+region which are expressed as well as deferentially accessible.
So for example here in this case in RNA seq data there is only one
SPON1 gene so if I have to show it associated region how to put that,shall I consider promoter or the distal intergenic or consider which is more significant.