Create a GRangesList object given a BEDset id

bb_to_grangeslist(bedbase, bedset_id, quietly = TRUE)

Arguments

bedbase: BEDbase() object
bedset_id: integer(1) BEDset record identifier
quietly: logical(1) (default TRUE) display messages

Value

GRangesList

Examples

bedbase <- BEDbase()
#> 125977 BED files available.
bedset_id <- "lola_hg38_ucsc_features"
bb_to_grangeslist(bedbase, bedset_id)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> GRangesList object of length 11:
#> [[1]]
#> GRanges object with 864 ranges and 0 metadata columns:
#>         seqnames            ranges strand
#>            <Rle>         <IRanges>  <Rle>
#>     [1]     chr1    690078-6272609      *
#>     [2]     chr1    690078-2326424      *
#>     [3]     chr1    771707-6806566      *
#>     [4]     chr1    771707-3153758      *
#>     [5]     chr1    805477-4942653      *
#>     ...      ...               ...    ...
#>   [860]     chrY 23762211-26011096      *
#>   [861]     chrY 23762211-26011096      *
#>   [862]     chrY 23774007-25910251      *
#>   [863]     chrY 26011096-26174983      *
#>   [864]     chrY 26312489-26653776      *
#>   -------
#>   seqinfo: 711 sequences (1 circular) from hg38 genome
#> 
#> ...
#> <10 more elements>