DropLoops: Drop loops from _LoopRanges_ objects using anchor and loop...

In LoopRig: Integration and Analysis of Chromatin Loop Data

Description

Subset loops based on loop and anchor size filters. Can be used to filter the loops in the LoopRanges object before or after calling ConsensusLoops

Usage

DropLoops(loop_ranges, type = NULL, size = NULL)

Arguments

loop_ranges	A LoopRanges class object
type	A string indicating the type of filtering when determining which loops to drop: "anchor_size" - Drops loops based on given anchor sizes "loop_size" - Drops loops based on end-to-end loop size
size	A numerical vector indicating size range to keep (e.g. c(start, end))

Value

A subsetted LoopRanges class object

Examples

# Load loops into LoopRanges object 
ovary_loops <- system.file("extdata/loops", "ovary_hg19.bedpe", 
package = "LoopRig", mustWork = TRUE) 
loops_ovary <- LoopsToRanges(ovary_loops, custom_cols = 0)

# Subset loops based on total length between 100 to 100000 bp 
DropLoops(loops_ovary, type = "loop_size", size = c(100, 100000))

# Subset loops based on anchor size between 1000 to 25000 bp 
DropLoops(loops_ovary, type = "anchor_size", size = c(1000, 25000))

LoopRig documentation built on Jan. 11, 2020, 9:27 a.m.