I am using ChIPseeker to annotate TF ChIP-seq peaks to gene. As mentioned in the article and tutorial, maximum distance cut-off can be used to annotate the peaks in
annotatePeak function. I guess
tssRegion is the option that can be used for max distance cut-off.
tssRegion cut-off would be helpful as reasoned
binding sites might be located between two start sites of different genes or hit different genes which have the same TSS location in the genome.
However it is not clear to what is the maximal distance cut-off for a peak to be assigned to a gene, or all peaks forced to be assigned to the closest gene even if the distance is too long?