Process ABC scores and save as a GRanges object

Process ABC scores and save as a GRanges object

process_ABC(
  ABC,
  gene.annots = NULL,
  full.element = FALSE,
  score.thresh = 0.015,
  flank = 0
)

Arguments

ABC

A data frame of ABC scores from Nasser et al. Nature 2021 paper

gene.annots

If provided, restrict to genes in gene.annots

full.element

Logical; if TRUE, use full length of ABC elements extracted from the "name" column. Otherwise, use the original (narrow) regions provided in the ABC scores data.

score.thresh

Numeric. Threshold of ABC scores. (default = 0.015, as in Nasser et al. Nature 2021 paper).

flank

Integer. Extend bases on both sides of the ABC elements (default = 0).

Value

a GRanges object with processed ABC scores, with genomic coordinates of the interacting regions and gene names (promoters).