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

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

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 = "/"))
#> [1] "BED file exported to C:\\Users\\Acer\\AppData\\Local\\Temp\\Rtmp0QOr1D/promoters_ex.bed"

# 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 = "/"))
#> [1] "BEDPE file exported to C:\\Users\\Acer\\AppData\\Local\\Temp\\Rtmp0QOr1D/ovary_loops_ex.bed"