Create a GRanges object given a BED id. Columns and types
are generated for broad and narrow peak files. Known columns and types can
be passed as a named vector through extra_cols. Otherwise,
bb_to_granges() attempts to determine the column type and substitute dummy
column names.
bb_to_granges(bedbase, bed_id, extra_cols = NULL, quietly = TRUE)bedbase <- BEDbase()
#> 130451 BED files available.
ex_bed <- bb_example(bedbase, "bed")
bb_to_granges(bedbase, ex_bed$id)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> GRanges object with 758 ranges and 6 metadata columns:
#> seqnames ranges strand | name score signalValue
#> <Rle> <IRanges> <Rle> | <character> <numeric> <numeric>
#> [1] chr1 1309757-1310040 * | <NA> 628 27.1098
#> [2] chr1 1361050-1361333 * | <NA> 969 46.9058
#> [3] chr1 1595600-1595883 * | <NA> 544 37.8757
#> [4] chr1 1596172-1596455 * | <NA> 1000 60.3260
#> [5] chr1 2896839-2897122 * | <NA> 670 27.9391
#> ... ... ... ... . ... ... ...
#> [754] chrX 137592599-137592882 * | <NA> 621 35.1752
#> [755] chrX 140723887-140724170 * | <NA> 570 20.7953
#> [756] chrX 140725202-140725485 * | <NA> 770 39.3965
#> [757] chrX 153382538-153382821 * | <NA> 586 37.2207
#> [758] chrY 11327531-11327814 * | <NA> 768 38.3850
#> pValue qValue peak
#> <numeric> <numeric> <integer>
#> [1] -1 -0.32846 142
#> [2] -1 -0.12926 142
#> [3] -1 -0.37348 142
#> [4] -1 0.33303 142
#> [5] -1 -0.34152 142
#> ... ... ... ...
#> [754] -1 -0.39023 142
#> [755] -1 -0.18003 142
#> [756] -1 -0.33490 142
#> [757] -1 -0.37418 142
#> [758] -1 -0.36814 142
#> -------
#> seqinfo: 711 sequences (1 circular) from hg38 genome