Process chromatin loop data and save as a GRanges object

Process chromatin loop data and save as a GRanges object

process_loop_data(loops, gene.annots = NULL, score.thresh = 0, flank = 0)

Arguments

loops

A data frame of chromatin loops, with columns: "chr", "start", "end", "gene_name", and "score" (optional).

gene.annots

If provided, restrict to genes in gene.annots

score.thresh

Numeric. Threshold of interaction scores. (default = 0).

flank

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

Value

A GRanges object with processed chromatin loops, with genomic coordinates of the regulatory elements and gene names.