Open zrcjessica opened 3 years ago
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
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