Calculate enrichment combinations of different elements within a list

Usage

combinations_enrichment(grlist, genome_size, ignore.strand = TRUE)

Arguments

grlist: Named list of GRanges objects
genome_size: Genome size
ignore.strand: If true, strand is not considered for 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 = "-")

enrichment <- combinations_enrichment(
  list("A" = gr_a1, "B" = gr_a2, "X" = gr_b1),
  genome_size = 30,
  ignore.strand = FALSE
)