detectNodes: Detect the interaction node

In jianhong/GenomicInteractionNodes: A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

Detect the interaction node

Description

Define the interaction node from input Pairs.

Usage

detectNodes(interaction, pval_cutoff = 0.05, ...)

Arguments

interaction	An object of Pairs to represent interactions.
pval_cutoff	Cutoff P value for interaction node by poisson distribution
...	Not used.

Value

A list of interaction nodes with elements: node_connection, Pairs object represent interactions interacted with nodes; nodes, GRanges object represent regions involved in nodes; node_regions, GRanges object represent regions interacted with nodes.

Examples

library(rtracklayer)
p <- system.file("extdata", "WT.2.bedpe",
                 package = "GenomicInteractionNodes")
interactions <- import(con=p, format="bedpe")
nodes <- detectNodes(interactions)

jianhong/GenomicInteractionNodes documentation built on Oct. 28, 2023, 1:11 a.m.