RegionGeneLinks: Compute relationship between arbitrary regions and genes...

In yanwu2014/chromfunks: Functions for Analyzing Chromatin Accessibility Data

Compute relationship between arbitrary regions and genes using either Hi-C or coaccessibility

Description

Compute relationship between arbitrary regions and genes using either Hi-C or coaccessibility

Usage

RegionGeneLinks(
  regions,
  conns,
  link.promoter = T,
  promoter.region = c(-3000, 3000),
  anno.level = "transcript",
  region.name = NULL,
  weight.col = NULL
)

Arguments

regions	Genomic regions in granges format
conns	Dataframe of peak to peak Hi-C/coaccessibility
link.promoter	Include peaks in gene promoters
promoter.region	Specify the window around the TSS that counts as a promoter
anno.level	Specify "gene" or "transcript" for a gene/transcript level annotation
region.name	Column name of region identifier. Defaults to peak names
weight.col	Column name of weights (i.e. when using coaccessibility). Defaults to 1

Value

Matrix of region to gene Hi-C/coaccessibility connections

yanwu2014/chromfunks documentation built on Aug. 20, 2023, 9:17 a.m.