I have been using ChipSeeker for a while now, but I am struggling with understanding how does the flanking gene feature in annotatePeak works.
First, are theses genes meant to flank the peak or the gene assigned to the peak.
Second, are the geneIDs entrez IDs
Third, the number of flanking genes I get (which is 72) does not match the number of elements I get in flank_gene_distance (which is only 42)?
And last, what does flanking distance of 0 means? As I tried to look at UCSC genome track, but there should not be any other genes overlapping the peak.
Thank you for all the help.