Extract LINE-1 methylation status from WGBS data
After a more extensive search, I found a useful answer that I'll share in case anyone else wonders how to do this. I'm using MethylKit package for differential methylation expression and it is quite easy to integrate with Genomic Ranges and rtracklayer in R to extract particular element methylation differences:

element.of.interest &lt;- import.bed("FILENAME.bed") #download custom track from Genome Browser
element.meth &lt;- diffmeth[as(diffmeth, "GRanges") %over% element.of.interest]


where "diffmeth" is the resulting MethylKit object from the differential methylation analysis.