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()
#> 665778 BED files available.
ex_bed <- bb_example(bedbase, "bed")
str(ex_bed)
#> List of 21
#> $ name : chr "ENCFF370XZK"
#> $ genome_alias : chr "hg38"
#> $ genome_digest : chr "Ba88PY52_qeifhJrgUXyin6UITdXNsg3"
#> $ bed_compliance : chr "bed5+1"
#> $ data_format : chr "bed_like_rs"
#> $ compliant_columns : int 5
#> $ non_compliant_columns: int 1
#> $ header : NULL
#> $ id : chr "0000143becc12fcd50c62f3d78fe7421"
#> $ description : chr "female adult (53 years)"
#> $ submission_date : chr "2026-04-09T19:40:03.413783Z"
#> $ last_update_date : chr "2026-04-14T18:46:25.972343Z"
#> $ 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 "adrenal gland"
#> ..$ cell_line : NULL
#> ..$ tissue : chr "endocrine gland, adrenal gland"
#> ..$ library_source : NULL
#> ..$ assay : chr "PRO-cap"
#> ..$ antibody : NULL
#> ..$ target : NULL
#> ..$ treatment : NULL
#> ..$ global_sample_id :List of 1
#> .. ..$ : chr "encode:ENCFF370XZK"
#> ..$ global_experiment_id:List of 1
#> .. ..$ : chr "encode:ENCSR970ACM"
#> ..$ original_file_name : chr "ENCFF370XZK.bed.gz"
#> $ processed : logi FALSE
#> $ stats : NULL
#> $ plots : NULL
#> $ files : NULL
#> $ universe_metadata : NULL
#> $ bedsets : NULL
ex_bedset <- bb_example(bedbase, "bedset")
str(ex_bedset)
#> List of 14
#> $ id : chr "encode_batch_1"
#> $ name : chr "encode_batch_1"
#> $ md5sum : chr "462eaea7176647244639b3c991b2a315"
#> $ submission_date : chr "2025-04-25T01:45:58.252912Z"
#> $ last_update_date: chr "2025-04-25T01:45:58.252916Z"
#> $ statistics :List of 2
#> ..$ mean:List of 19
#> .. ..$ number_of_regions : num 147624
#> .. ..$ gc_content : num 0.505
#> .. ..$ median_tss_dist : num 33829
#> .. ..$ mean_region_width : num 352
#> .. ..$ exon_frequency : num 7287
#> .. ..$ exon_percentage : num 0.0491
#> .. ..$ intron_frequency : num 61340
#> .. ..$ intron_percentage : num 0.354
#> .. ..$ intergenic_percentage : num 0.344
#> .. ..$ intergenic_frequency : num 58875
#> .. ..$ promotercore_frequency : num 4825
#> .. ..$ promotercore_percentage: num 0.0798
#> .. ..$ fiveutr_frequency : num 5052
#> .. ..$ fiveutr_percentage : num 0.0947
#> .. ..$ threeutr_frequency : num 5509
#> .. ..$ threeutr_percentage : num 0.0358
#> .. ..$ promoterprox_frequency : num 4736
#> .. ..$ promoterprox_percentage: num 0.0418
#> .. ..$ distributions : NULL
#> ..$ sd :List of 19
#> .. ..$ number_of_regions : num 131857
#> .. ..$ gc_content : num 0.0671
#> .. ..$ median_tss_dist : num 29802
#> .. ..$ mean_region_width : num 247
#> .. ..$ exon_frequency : num 7941
#> .. ..$ exon_percentage : num 0.0269
#> .. ..$ intron_frequency : num 59158
#> .. ..$ intron_percentage : num 0.132
#> .. ..$ intergenic_percentage : num 0.132
#> .. ..$ intergenic_frequency : num 58988
#> .. ..$ promotercore_frequency : num 3475
#> .. ..$ promotercore_percentage: num 0.0895
#> .. ..$ fiveutr_frequency : num 3235
#> .. ..$ fiveutr_percentage : num 0.147
#> .. ..$ threeutr_frequency : num 6369
#> .. ..$ threeutr_percentage : num 0.0241
#> .. ..$ promoterprox_frequency : num 4000
#> .. ..$ promoterprox_percentage: num 0.026
#> .. ..$ distributions : NULL
#> $ distributions : NULL
#> $ plots :List of 1
#> ..$ region_commonality: NULL
#> $ description : chr "Encode project for hg38 genome filtered on files size < 20 mb"
#> $ summary : NULL
#> $ bed_ids :List of 994
#> ..$ : chr "000f4769cb6875314ea496302f8b0116"
#> ..$ : chr "004749fdf8933f6de8399fa1f2ae3bcb"
#> ..$ : chr "004bc471a80de4aaefe7c5d848491da5"
#> ..$ : chr "0065059bb8c3d1e3c842cb67aca480b7"
#> ..$ : chr "007603c2bc504cc08b013530d81bb39b"
#> ..$ : chr "0089ba0766bb475bef45cc0325c8471a"
#> ..$ : chr "009c9b4d82765bd487eb3a28713d62e2"
#> ..$ : chr "00cf0a376a51298f66d7e49fd7b56d62"
#> ..$ : chr "00db6e5b06c8fde0faebb7b361c2a8fe"
#> ..$ : chr "00e15bf26ead13933e83ef3124b6b4b4"
#> ..$ : chr "010cc74377b4f381078affbc726360df"
#> ..$ : chr "010fbbf4aa5bfdb07ba2bfd9265ee1cf"
#> ..$ : chr "011e13c165d768480e152716f678bf12"
#> ..$ : chr "018cfa2c47249f966c1cf0a8145aa6b2"
#> ..$ : chr "01b391da54e2a9ffe723de432b7d53dd"
#> ..$ : chr "01d49bf4ee24dac74f81015fe57ce34c"
#> ..$ : chr "01f37848395d17f08a3fceef18ee6f5d"
#> ..$ : chr "025632a0aad9b01543f6415c471995bd"
#> ..$ : chr "0316154c3ad1e49506aefbecfad80922"
#> ..$ : chr "0346740a76ba8f28efb99fa284ff92fc"
#> ..$ : chr "0346ea63de762b852f16cf312db5c8db"
#> ..$ : chr "034a76460b5e111b73978aab17b4913d"
#> ..$ : chr "0373dabcc9d4f422814add26faa6822a"
#> ..$ : chr "037bd8e2c9d0c82cea0389d5b163ce34"
#> ..$ : chr "03effe9100b67896e826a2051091eb1c"
#> ..$ : chr "0432a954dbf060387eb7fa6997ce322f"
#> ..$ : chr "04aa524ee65b59408b057dafee1e7c53"
#> ..$ : chr "04add9757b6bd272e3db56deb6779882"
#> ..$ : chr "04f7f0768d763ddc4b70757b80251a70"
#> ..$ : chr "04f9af9930577865775a6d49331828ab"
#> ..$ : chr "053d6f31429e1ebbe7c243a5f321b119"
#> ..$ : chr "054279c87e07890bb15a9462fceb7672"
#> ..$ : chr "055b118d342902fdb2d340940e2fbcd8"
#> ..$ : chr "057bcd00a0c85a8a4a5693bed2754dea"
#> ..$ : chr "059151bdf0c3580b2f533e65f434acff"
#> ..$ : chr "05a56337d9ea39e542468294b95efeac"
#> ..$ : chr "05e9657e1c8f5657f52fcb2e14f1a834"
#> ..$ : chr "067613bf1f99f296b67978cf50882975"
#> ..$ : chr "068998436ac80518e6a633dfcfb098df"
#> ..$ : chr "06dc4b5281b3653c2fa3cf918a5af787"
#> ..$ : chr "06ea933c8ea33e97e84782c350c84235"
#> ..$ : chr "073ed8df4352a8b7f45cd0956c3dcda9"
#> ..$ : chr "0774b0a67de3e3d49ed55a9d7dc7fcf6"
#> ..$ : chr "07816a5bf20dc754f1e18bcdb5dec6ec"
#> ..$ : chr "07a773aefadf4c2528ea945e1a58b2dd"
#> ..$ : chr "07dfbc9f730333a1dfd5425ac9c6c775"
#> ..$ : chr "0831c46bfd934745d5a1cceb06f201b8"
#> ..$ : chr "087bda10709bff52aff6b2d33feee75f"
#> ..$ : chr "08e816aee75ae181fdd04fda5d4e59e1"
#> ..$ : chr "08ec2b2ed890795b6ae193df5ac093fa"
#> ..$ : chr "090e819f95f28fd218d712f6ccc3cb2a"
#> ..$ : chr "09309155aa1fedc2c486592afc0ae35e"
#> ..$ : chr "096d920bb3db0fe348fe1f86c9d881a4"
#> ..$ : chr "099297708b5203a4552a326438dd0a32"
#> ..$ : chr "09f45c3dd98ccfe7dd4605475b1fd5aa"
#> ..$ : chr "0a2e57e7cf76d3eec0b33077c927f2f6"
#> ..$ : chr "0a51645ef3a24ba8cbea3ec43adf7b2a"
#> ..$ : chr "0a96793ce91b7aaddc3618c74ddb4359"
#> ..$ : chr "0ac99158ab5a2983cb9ced7cb58f6712"
#> ..$ : chr "0ae33233043e705bb141b70b4c4b88aa"
#> ..$ : chr "0b85b43047b6d876a8994e99151b83ae"
#> ..$ : chr "0bb1f9da4e4586d8f4c416e6f73b4fc2"
#> ..$ : chr "0c23e990b2e146004cbf4584c97e99c3"
#> ..$ : chr "0c566454f35ee39c0adec7146af9a510"
#> ..$ : chr "0ca628a095a1607149e9e19c2e8cd90d"
#> ..$ : chr "0caeb7f90602a6e331d5e7ca328f0c96"
#> ..$ : chr "0cded12d0618d0454837aee383e1cd69"
#> ..$ : chr "0d033d245b38a27a128495521800043d"
#> ..$ : chr "0da67b9ea1c2d4c9bafe05d9ebd040ac"
#> ..$ : chr "0e03fa0d5a4d2d94ddd9c5af8e490220"
#> ..$ : chr "0e8b5813fdf5b406bc873ace022f023d"
#> ..$ : chr "0eae82771627a0212f1557a69d594288"
#> ..$ : chr "0eb4cf8dadb0db5cecb1c8475be99fe9"
#> ..$ : chr "0ec52382b31f94e479024b5f5c29ba87"
#> ..$ : chr "0ef2957a32cfb0aaa78dd0ac6a53170b"
#> ..$ : chr "0efe5691e23c8c90eab2823902b8c228"
#> ..$ : chr "0f48a8559f47ed628e88dfdf72483d29"
#> ..$ : chr "0f5d1e8a1d0ef5dfadc65e15845bfd7a"
#> ..$ : chr "0f7ae2a396a3a0a74511ac466fce24b9"
#> ..$ : chr "0f80de6688f65d05dee3562c0c3561ad"
#> ..$ : chr "0f8d5d0c659a820b3fe3142d77ab4067"
#> ..$ : chr "0fb5ec8bd98dc2b0e89d74f9c768ef7f"
#> ..$ : chr "10145a8813b39dd69e0af7c7efede836"
#> ..$ : chr "102bfd56f57fe278f82b33853028413b"
#> ..$ : chr "1114b74ba44305960b9a5e5479a2ec0d"
#> ..$ : chr "112228491e00d5944e44ba66e2b75a17"
#> ..$ : chr "1123a065483eb1a4417a41c6bae9b7c0"
#> ..$ : chr "114deae9598ef8f2bd3e3da7fddf4a5c"
#> ..$ : chr "1177e84293d19b7634e2bd369b91901d"
#> ..$ : chr "11a8d774d24e4893c18965fe2b66f1ed"
#> ..$ : chr "11b8862a94595b889ddf710a6063af1e"
#> ..$ : chr "11faca2afe4f4d85b72bb345b0dd3359"
#> ..$ : chr "12018363b3589c26d3c438d5384a0440"
#> ..$ : chr "120e717dd0a86d3f002ad401a000acc7"
#> ..$ : chr "122d7a5f0d61727c9573b7d557889587"
#> ..$ : chr "126d5e7e0651d8da3590bab21fbdf082"
#> ..$ : chr "1271a20deffd80c509f06b2af96aa4f5"
#> ..$ : chr "12ed7f81370576c2d65a389a4992f39b"
#> ..$ : chr "1310bba871be999e04172411d696dbaf"
#> .. [list output truncated]
#> $ bedfile_count : int 994
#> $ author : NULL
#> $ source : NULL