Export GInteractions as bedpe or pairs files — ginteractions-export • plyinteractions

write_* functions are provided to export a GInteractions object into these two file formats. See 4DN documentation (https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md) and UCSC documentation (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format) for more details.

Usage

write_bedpe(x, file, scores = NULL)

write_pairs(x, file, seqlengths = GenomeInfoDb::seqlengths(x))

Arguments

x: a GInteractions object.
file: path to a .bedpe or .pairs file to save the genomic interactions.
scores: Name of column to extract scores from.
seqlengths: Named vector indicating the chromosome sizes.

Value

TRUE

Examples

gi <- read.table(text = "
chr1 100 200 chr1 5000 5100 bedpe_example1 30 + -
chr1 1000 5000 chr1 3000 3800 bedpe_example2 100 + -",
col.names = c(
  "seqnames1", "start1", "end1", 
  "seqnames2", "start2", "end2", "name", "score", "strand1", "strand2")
) |> as_ginteractions()

write_bedpe(gi, 'gi.bedpe')
#> [1] TRUE
write_pairs(gi, 'gi.pairs')
#> No `seqlengths` provided. The `chromsizes` will be inferred from the interactions and will most likely be inaccurate.
#> [1] TRUE