Get the example BED file or BEDset available through bedhost. Useful for an initial exploration of bedbaser with an example BED file and BEDset in BEDbase.
bb_example(bedbase, rec_type = c("bed", "bedset"))list() bed files or bedsets
bedbase <- BEDbase()
#> 125977 BED files available.
ex_bed <- bb_example(bedbase, "bed")
str(ex_bed)
#> List of 22
#> $ name : chr "encode_10240"
#> $ genome_alias : chr "hg38"
#> $ genome_digest : chr "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
#> $ bed_compliance : chr "bed6+3"
#> $ data_format : chr "encode_broadpeak"
#> $ compliant_columns : int 6
#> $ non_compliant_columns: int 3
#> $ header : NULL
#> $ id : chr "afbdec2bd8ff7f22467a39d6146d1714"
#> $ description : chr "GM DNase-seq experiment on K562 (Blast phase chronic myelogenous leukemia, BCR-ABL1 positive cell line from pleural effusion)"
#> $ submission_date : chr "2025-04-28T23:15:53.132875Z"
#> $ last_update_date : chr "2025-07-18T20:52:00.968951Z"
#> $ is_universe : logi FALSE
#> $ license_id : chr "DUO:0000042"
#> $ annotation :List of 16
#> ..$ species_name : chr "Homo sapiens"
#> ..$ species_id : chr "9606"
#> ..$ genotype : chr ""
#> ..$ phenotype : chr ""
#> ..$ description : chr ""
#> ..$ cell_type : chr ""
#> ..$ cell_line : chr "K562"
#> ..$ tissue : chr ""
#> ..$ library_source : chr "genomic"
#> ..$ assay : chr "DNase-Hypersensitivity"
#> ..$ antibody : chr ""
#> ..$ target : chr ""
#> ..$ treatment : chr ""
#> ..$ global_sample_id :List of 2
#> .. ..$ : chr "encode:ENCFF708QSW"
#> .. ..$ : chr "geo:gsm2400267"
#> ..$ global_experiment_id:List of 2
#> .. ..$ : chr "encode"
#> .. ..$ : chr "geo:gse90287"
#> ..$ original_file_name : chr "GSM2400267_ENCFF708QSW_hotspots_GRCh38.bed.gz"
#> $ processed : logi TRUE
#> $ stats : NULL
#> $ plots : NULL
#> $ files : NULL
#> $ universe_metadata : NULL
#> $ raw_metadata : NULL
#> $ bedsets : NULL
ex_bedset <- bb_example(bedbase, "bedset")
str(ex_bedset)
#> List of 12
#> $ id : chr "gse127704"
#> $ name : chr "gse127704"
#> $ md5sum : chr "b509b959846303ecba35adc66e7838ff"
#> $ submission_date : chr "2025-06-03T16:17:24.565586Z"
#> $ last_update_date: chr "2025-06-03T16:17:24.565590Z"
#> $ statistics :List of 2
#> ..$ mean:List of 18
#> .. ..$ number_of_regions : num 3e+05
#> .. ..$ gc_content : num 0.435
#> .. ..$ median_tss_dist : num 37110
#> .. ..$ mean_region_width : num 362
#> .. ..$ exon_frequency : num 10536
#> .. ..$ exon_percentage : num 0.0352
#> .. ..$ intron_frequency : num 132950
#> .. ..$ intron_percentage : num 0.443
#> .. ..$ intergenic_percentage : num 0.424
#> .. ..$ intergenic_frequency : num 127308
#> .. ..$ promotercore_frequency : num 3364
#> .. ..$ promotercore_percentage: num 0.0113
#> .. ..$ fiveutr_frequency : num 6050
#> .. ..$ fiveutr_percentage : num 0.0202
#> .. ..$ threeutr_frequency : num 8175
#> .. ..$ threeutr_percentage : num 0.0273
#> .. ..$ promoterprox_frequency : num 11616
#> .. ..$ promoterprox_percentage: num 0.0387
#> ..$ sd :List of 18
#> .. ..$ number_of_regions : num 0
#> .. ..$ gc_content : num 0.0071
#> .. ..$ median_tss_dist : num 651
#> .. ..$ mean_region_width : num 2.27
#> .. ..$ exon_frequency : num 614
#> .. ..$ exon_percentage : num 0.0021
#> .. ..$ intron_frequency : num 96.9
#> .. ..$ intron_percentage : num 4e-04
#> .. ..$ intergenic_percentage : num 0.0011
#> .. ..$ intergenic_frequency : num 315
#> .. ..$ promotercore_frequency : num 483
#> .. ..$ promotercore_percentage: num 0.0016
#> .. ..$ fiveutr_frequency : num 552
#> .. ..$ fiveutr_percentage : num 0.0018
#> .. ..$ threeutr_frequency : num 885
#> .. ..$ threeutr_percentage : num 0.0029
#> .. ..$ promoterprox_frequency : num 53
#> .. ..$ promoterprox_percentage: num 1e-04
#> $ plots :List of 1
#> ..$ region_commonality: NULL
#> $ description : chr "Data from [GEO GSE127704](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127704)\nChIP-seq from K562 (ENCSR497VFH)"
#> $ summary : NULL
#> $ bed_ids :List of 4
#> ..$ : chr "3b56d2689a821ef80da854e789e7c4bc"
#> ..$ : chr "4704124ec926afd6c557536f3ddd266a"
#> ..$ : chr "58114a3e44dea03decaa305f35c0f60b"
#> ..$ : chr "9a2adba03018d2e8780fb743a7d7dc3c"
#> $ author : chr "ENCODE, DCC"
#> $ source : chr "gse127704"