Reads a standard BEDPE file and converts it into a Bioconductor
GInteractions object.
Value
A GInteractions object with a score metadata column
(defaulting to 0 if not provided).
Details
Anchor Normalization:
Anchor order is automatically normalized so that the first anchor is
lexicographically less than or equal to the second (e.g., chr1 < chr2),
ensuring compatibility with GInteractions(mode = "strict").
Score Detection: The function attempts to automatically detect a numeric score column. It checks the 8th column first (standard for many tools); if not numeric, it falls back to the 7th column. Non-numeric values are treated as 0.
Examples
# 1. Locate the example BEDPE file included in the package
# system.file finds the absolute path to 'inst/extdata/example_loops_1.bedpe'
bedpe_path <- system.file("extdata", "example_loops_1.bedpe", package = "looplook")
# 2. Run the function (ensure file was found)
if (bedpe_path != "") {
gi <- bedpe_to_gi(bedpe_path)
# 3. Inspect the result
print(gi)
# Check the imported score column
S4Vectors::mcols(gi)$score
}
#> StrictGInteractions object with 300 interactions and 1 metadata column:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] chr1 109492652-109495835 --- chr1 110644072-110649627 |
#> [2] chr1 116687216-116689300 --- chr1 116844969-116856809 |
#> [3] chr1 116876465-116881376 --- chr1 117819956-117830132 |
#> [4] chr1 146374138-146379497 --- chr1 146442737-146445345 |
#> [5] chr1 1370034-1377149 --- chr1 1469037-1474411 |
#> ... ... ... ... ... ... .
#> [296] chr1 1011273-1015982 --- chr1 1018256-1022868 |
#> [297] chr1 1342739-1364987 --- chr1 1397119-1403614 |
#> [298] chr1 147271364-147274896 --- chr1 147290756-147294529 |
#> [299] chr1 108639596-108642391 --- chr1 109098569-109102247 |
#> [300] chr1 11011474-11014295 --- chr1 12745038-12747130 |
#> score
#> <numeric>
#> [1] 1
#> [2] 1
#> [3] 2
#> [4] 1
#> [5] 3
#> ... ...
#> [296] 12
#> [297] 7
#> [298] 4
#> [299] 1
#> [300] 1
#> -------
#> regions: 385 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> [1] 1 1 2 1 3 1 2 8 3 1 1 4 2 1 1 1 1 1
#> [19] 2 8 3 1 1 1 1 219 7 2 1 1 2 1 1 1 1 1
#> [37] 1 3 1 1 2 44 1 1 2 4 1 1 1 3 1 1 5 2
#> [55] 1 1 3 2 1 1 3 1 1 1 1 1 1 5 1 2 1 1
#> [73] 1 2 1 2 5 1 2 1 1 1 1 1 2 1 1 1 8 1
#> [91] 3 1 1 2 3 1 1 2 2 1 1 1 1 1 1 1 1 1
#> [109] 11 7 1 9 1 1 1 1 1 1 1 2 1 3 3 1 2 1
#> [127] 2 1 1 2 1 1 1 1 4 1 1 1 1 1 3 1 3 2
#> [145] 7 1 1 1 2 3 1 2 2 1 2 9 1 2 5 1 3 4
#> [163] 1 8 1 1 1 3 1 1 1 7 7 1 2 1 2 1 5 1
#> [181] 1 1 1 1 1 2 5 1 1 1 12 2 1 1 1 1 2 14
#> [199] 2 1 1 1 33 1 1 1 1 4 1 1 1 2 1 36 1 3
#> [217] 2 1 1 2 2 1 1 1 1 5 10 1 1 1 1 1 3 36
#> [235] 1 2 1 3 1 1 2 1 1 3 1 1 2 5 1 1 1 3
#> [253] 1 9 2 1 1 1 1 4 1 1 9 1 2 4 1 2 1 1
#> [271] 1 19 1 10 1 2 2 1 10 1 1 2 1 1 3 1 1 1
#> [289] 1 4 1 1 2 1 2 12 7 4 1 1