List BEDs

List BED files available through bedhost. By default uses the bedhost default of 1000 records and an initial offset of 0.

bb_list_beds(
  bedbase,
  genome = NULL,
  bed_compliance = NULL,
  limit = 1000,
  offset = 0
)

Arguments

bedbase

BEDbase() object

genome

character(1) (default NULL) genome keyword

bed_compliance

character(1) (default NULL) bed compliance, e.g., 'bed6+4'

limit

integer(1) (default 1000) maximum records

offset

integer(1) (default 0) page token of records

Value

tibble of BED records

Examples

bedbase <- BEDbase()
#> 663721 BED files available.
bb_list_beds(bedbase)
#> # A tibble: 1,000 × 51
#>    name  genome_alias genome_digest bed_compliance data_format compliant_columns
#>    <chr> <chr>        <chr>         <chr>          <chr>       <chr>            
#>  1 Plas… hg19         GOIHeGSorDrb… bed6+4         encode_nar… 6                
#>  2 ENCF… hg38         Ba88PY52_qei… bed5+1         bed_like_rs 5                
#>  3 ENCF… hg38         Ba88PY52_qei… bed4+1         bed_like    4                
#>  4 ENCF… hg38         Ba88PY52_qei… bed4+1         bed_like    4                
#>  5 ENCF… hg38         Ba88PY52_qei… bed6+3         encode_bro… 6                
#>  6 ENCF… hg38         Ba88PY52_qei… bed4+1         bed_like    4                
#>  7 ENCF… hg38         Ba88PY52_qei… bed4+1         bed_like    4                
#>  8 ENCF… hg38         Ba88PY52_qei… bed4+0         ucsc_bed    4                
#>  9 ENCF… hg38         Ba88PY52_qei… bed4+1         bed_like    4                
#> 10 ENCF… hg38         Ba88PY52_qei… bed4+1         bed_like    4                
#> # ℹ 990 more rows
#> # ℹ 45 more variables: non_compliant_columns <chr>, id <chr>,
#> #   description <chr>, submission_date <chr>, last_update_date <chr>,
#> #   is_universe <chr>, license_id <chr>, annotation.organism <chr>,
#> #   annotation.species_id <chr>, annotation.genotype <chr>,
#> #   annotation.phenotype <chr>, annotation.description <chr>,
#> #   annotation.cell_type <chr>, annotation.cell_line <chr>, …