LoopsToRanges: Create a list of ranges objects from looping data

In LoopRig: Integration and Analysis of Chromatin Loop Data

Description

Uses tab delimited looping data in the form of BEDPE files to create custom GRanges loop objects

Usage

LoopsToRanges(..., loop_names = NULL, custom_cols = 0,
  custom_mcols = NULL)

Arguments

...	Any number of tab delimited loop data files in BEDPE format
loop_names	A character vector of names for the loop datasets (optional)
custom_cols	An integer indicating the number of extra columns in the BEDPE file (default = 0)
custom_mcols	An integer or vector of integers indicating which columns are used for metadata (optional)

Value

A LoopRanges class object: list of GRanges looping data objects

Examples

# Load loops into LoopRanges object 
ovary_loops <- system.file("extdata/loops", "ovary_hg19.bedpe", 
package = "LoopRig", mustWork = TRUE) 
spleen_loops <- system.file("extdata/loops", "spleen_hg19.bedpe", 
package = "LoopRig", mustWork = TRUE)
LoopsToRanges(ovary_loops, spleen_loops, custom_cols = 0)

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