add support for peak regions for ASOC analysis

[zrcjessica]

• ASOC analysis needs additional BED file for each sample that indicates peak regions found in each sample
• modify prepare_counts-rna.r and create a version (prepare_counts-atac.r?) that finds overlaps with peak regions instead of genes and reads in BED files instead of GTF file

[aryarm]

just attaching an excerpt from our Slack convo about this for the sake of archiving things:

yeah, so in this little section, we use findOverlaps to intersect the chr:start-end of the SNPs with the chr:start-end of the genes in the GTF file
so instead, we'd probably want to do the same thing but with a bed file instead of a GTF file
and here's where the GTF gets read into a Granges object
so we would probably just want to read the BED file into a Granges object using rtracklayer's import() function, instead

[aryarm]

update 4/6:
see this pr and this pr for preliminary work on this
it's still unclear as to whether the new config options I added will work with rna-seq, so that's why I'm not marking this as completed yet
we need a test dataset to try things out