Description Usage Arguments Examples
Uses ElementRanges objects to output to BED format, and LoopRanges objects to output to BEDPE format
1 |
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 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | # 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 = "/"))
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