LOLA runLOLA-regionDB to use for tissue-specific TFBS

[shanie-landen]

I would like to test for enrichment of skeletal muscle TFBS in my differentially methylated regions (DMRs).

I have a Granges object of my DMRs.
I have a Granges object of all of my tested CpGs (is this correct for the userUniverse?)
And for the regionDB I have come up with two options:

1. Load Cache of TFBS from Lola, but is there a way to select for skeletal muscle? (my Granges are annotated to hg38) In any case, haven't been able to figure out how to load the TFBS in the Cache, just the "extdata" example from the vignette, what are the options for "extdata" in -- dbPath = system.file("extdata", "hg19", package="LOLA")
2. Create my own- I have 4 bed files that I have downloaded from Unibind, is this the best way to achieve what I am trying to do? (I have done this but am not sure about the results, see screenshot below, also the FDR function from qvalue gives an error when runLOLA)
   Also-is there a way to filter out all of the TFBS annotated to the X and Y chromosomes from the 4 bed files at once?
   

Please advise if I am using this package correctly and if the results look normal.

Also I am concerned that using this method doesn't account for the multiple probe and gene bias issues in the EPIC array (see https://www.biorxiv.org/content/10.1101/2020.08.24.265702v1.abstract). But that is a whole other thing.

Lastly, what is the code to analyze for enrichment of all encode TFBS? I can't seem to figure out the input.
Thanks in advance!