Calculate pairwise enrichment matrix between two lists of GRanges objects

Usage

pairwise_enrichment(grlist_1, grlist_2, genome_size, ignore.strand = TRUE)

Arguments

grlist_1: A named list of GRanges
grlist_2: A named list of GRanges
genome_size: Genome size
ignore.strand: Ignore strand to calculate overlaps.

Value

A data frame in long format with the enrichment values calculated per pair.

Examples

gr_a1 <- GenomicRanges::GRanges(seqnames = c("chr1"), IRanges::IRanges(11, 20), strand = "-")
gr_a2 <- GenomicRanges::GRanges(seqnames = c("chr1"), IRanges::IRanges(24, 25), strand = "+")

gr_b1 <- GenomicRanges::GRanges(seqnames = c("chr1"), IRanges::IRanges(15, 24), strand = "-")
gr_b2 <- GenomicRanges::GRanges(seqnames = c("chr1"), IRanges::IRanges(16, 25), strand = "+")

gsize <- 30

enrichment <- pairwise_enrichment(
  list("A" = gr_a1, "B" = gr_a2),
  list("X" = gr_b1, "Y" = gr_b2),
  genome_size = gsize,
  ignore.strand = FALSE
)