ElementsToRanges: Create a list of ranges objects from element data

In LoopRig: Integration and Analysis of Chromatin Loop Data

Description

Uses tab delimited element data in the form of BED4 or BED12 files to create GRanges element objects

Usage

ElementsToRanges(..., element_names = NULL, custom_cols = NULL,
  custom_mcols = NULL)

Arguments

...	Any number of tab delimited element data files in BED4 or BED12 format
element_names	A character vector of names for the element datasets (optional)
custom_cols	An integer indicating the number of extra columns in the BED file.
custom_mcols	An integer or vector of integers indicating which columns are used for metadata (optional)

Value

An ElementRanges class object: list of GRanges element data objects

Examples

# Load enhancer and promoter elements into an ElementRanges object
enhancers <- system.file("extdata/elements", "enhancers.bed", package = "LoopRig", mustWork = TRUE)
promoters <- system.file("extdata/elements", "promoters.bed", package = "LoopRig", mustWork = TRUE)
element_ranges <- ElementsToRanges(enhancers, promoters, 
element_names = c("enhancers", "promoters"), 
custom_cols = 1, custom_mcols = 4)
element_ranges

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