Process PC-HiC data and save as a GRanges object

Process PC-HiC data and save as a GRanges object

process_pcHiC(pcHiC, gene.annots = NULL, score.thresh = 0, flank = 0)

Arguments

pcHiC

A data frame of PC-HiC data, with columns of enhancer"Promoter" and "Interacting_fragment". Interacting_fragment should contains chr, start and end positions of the fragments interacting with promoters e.g. "chr.start.end" or "chr:start-end".

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 PC-HiC links, with genomic coordinates of the interacting regions and gene names (promoters).