ExportBED {LoopRig}

Export a LoopRanges or italicsElementRanges object to a BED/BEDPE file

Description

Uses ElementRanges objects to output to BED format, and LoopRanges objects to output to BEDPE format

Usage

ExportBED(obj, index = NULL, mcol = FALSE, file_name)

Arguments

obj

An object of italicsLoopRanges or italicsElementRanges class

index

List index of LoopRanges or ElementRanges object to output

mcol

A boolean specifying whether the first mcol of the object are to be output (default=FALSE)

file_name

A string indicating the name and save location of the BED/BEDPE file

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)

# Call temporary directory 
tempdir <- tempdir()

# Export enhancers into temporary directory 
ExportBED(element_ranges, index = 1, file_name = paste(tempdir, "promoters_ex.bed", sep = "/"))

# 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)
pancreas_loops <- system.file("extdata/loops", "pancreas_hg19.bedpe", 
package = "LoopRig", mustWork = TRUE)
loops <- LoopsToRanges(ovary_loops, spleen_loops, pancreas_loops, custom_cols = 0)

# Export ovary loops into temporary directory 
ExportBED(loops, index = 1, file_name = paste(tempdir, "ovary_loops_ex.bed", sep = "/"))