process_loop_data: Process chromatin loop data and save as a GRanges object

In kevinlkx/mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Process chromatin loop data and save as a GRanges object

Description

Process chromatin loop data and save as a GRanges object

Usage

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.

kevinlkx/mapgen documentation built on March 31, 2024, 11:03 p.m.