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()
#> 128999 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 41694 ranges and 6 metadata columns:
#> seqnames ranges strand | name score
#> <Rle> <IRanges> <Rle> | <character> <numeric>
#> [1] chr1 86935-87280 * | Peak_3616 148
#> [2] chr1 880351-881297 * | Peak_3441 149
#> [3] chr1 883981-884420 * | Peak_51321 60
#> [4] chr1 897321-897632 * | Peak_39606 66
#> [5] chr1 914015-914745 * | Peak_130636 41
#> ... ... ... ... . ... ...
#> [41690] chrX 153829326-153829847 * | Peak_33691 71
#> [41691] chrX 153831173-153831489 * | Peak_72205 55
#> [41692] chrX 153885158-153885865 * | Peak_43424 66
#> [41693] chrX 154751539-154751827 * | Peak_13276 95
#> [41694] chrX 155863388-155863951 * | Peak_123283 43
#> signalValue pValue qValue peak
#> <numeric> <numeric> <numeric> <integer>
#> [1] 4.12363 14.87206 11.48560 176
#> [2] 4.57585 14.98495 11.57899 188
#> [3] 2.89001 6.09145 3.57573 264
#> [4] 3.01043 6.63229 4.03133 176
#> [5] 2.40834 4.10604 1.98388 455
#> ... ... ... ... ...
#> [41690] 3.13085 7.18963 4.50966 307
#> [41691] 2.76960 5.56772 3.14046 51
#> [41692] 3.01043 6.63229 4.03133 385
#> [41693] 3.61252 9.57284 6.61083 99
#> [41694] 2.35793 4.35143 2.19496 203
#> -------
#> seqinfo: 711 sequences (1 circular) from hg38 genome