I want to test differentially methylated regions (DMRs; identified in whole genome bisulfite sequencing data) for enrichment of certain genomic features. For example, do I see more DMRs in promoters than I would expect by chance?
It was suggested to me that a simple and first analysis could be done using the Homer function annotatePeaks.pl with the hidden option -annStats.
However, I want to provide a background list of all regions identified in the data.
Currently I'm running this:
annotatePeaks.pl dmrs_fdr.bed mm10 -annStats dmrs_enrich_homer.txt > annotated_dmrs_homer.txt
With dmrs_fdr.bed being the list of significant DMRs I want to test. However, this does not define the background list I want to test against.
Is it even possible to do this with homer?