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()
#> 125977 BED files available.
bb_list_beds(bedbase)
#> # A tibble: 1,000 × 52
#>    name                genome_alias bed_compliance data_format compliant_columns
#>    <chr>               <chr>        <chr>          <chr>       <chr>            
#>  1 Plasma B cells - T… "hg38"       bed6+4         encode_nar… 6                
#>  2 Young_Daughter 3y3A "mm10"       bed5+5         bed_like_rs 5                
#>  3 DU01: Damage H2AK1… ""           bed6+0         ucsc_bed    6                
#>  4 total RNA at diagn… "hg19"       bed4+2         bed_like    4                
#>  5 encode_16468        "hg38"       bed6+4         encode_nar… 6                
#>  6 Human colon cancer… "hg19"       bed6+3         encode_bro… 6                
#>  7 FGFR1(RA)_ChIP_Seq  "mm10"       bed6+4         encode_nar… 6                
#>  8 encode_4362         "hg38"       bed6+4         encode_nar… 6                
#>  9 TF ChIP-seq from H… "hg38"       bed6+4         encode_nar… 6                
#> 10 H3K4me3 Wnt3KO Chi… "mm9"        bed6+4         encode_nar… 6                
#> # ℹ 990 more rows
#> # ℹ 47 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>, …