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()
#> 168207 BED files available.
ex_bed <- bb_example(bedbase, "bed")
str(ex_bed)
#> List of 22
#> $ name : chr "encode_2074"
#> $ genome_alias : chr "hg38"
#> $ genome_digest : chr "Ba88PY52_qeifhJrgUXyin6UITdXNsg3"
#> $ bed_compliance : chr "bed6+3"
#> $ data_format : chr "encode_broadpeak"
#> $ compliant_columns : int 6
#> $ non_compliant_columns: int 3
#> $ header : NULL
#> $ id : chr "ee0c316f02b443c27b0136cb85c113c5"
#> $ description : chr "DNase-seq experiment on SJSA1 (Osteosarcoma cell line from femur)"
#> $ submission_date : chr "2025-04-24T23:25:31.252448Z"
#> $ last_update_date : chr "2026-02-08T09:56:25.908938Z"
#> $ 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 "SJSA1"
#> ..$ tissue : chr ""
#> ..$ library_source : chr ""
#> ..$ assay : chr "DNase-seq"
#> ..$ antibody : chr ""
#> ..$ target : chr ""
#> ..$ treatment : chr ""
#> ..$ global_sample_id :List of 1
#> .. ..$ : chr "encode:ENCFF209ZHV"
#> ..$ global_experiment_id:List of 1
#> .. ..$ : chr "encode"
#> ..$ original_file_name : chr "ENCFF209ZHV.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 "gse120532"
#> $ name : chr "gse120532"
#> $ md5sum : chr "cd04e239d745b9f97697781c20c4cd28"
#> $ submission_date : chr "2025-05-22T21:34:03.063062Z"
#> $ last_update_date: chr "2025-05-22T21:34:03.063068Z"
#> $ statistics :List of 2
#> ..$ mean:List of 18
#> .. ..$ number_of_regions : num 32996
#> .. ..$ gc_content : NULL
#> .. ..$ median_tss_dist : NULL
#> .. ..$ mean_region_width : num 795
#> .. ..$ exon_frequency : NULL
#> .. ..$ exon_percentage : NULL
#> .. ..$ intron_frequency : NULL
#> .. ..$ intron_percentage : NULL
#> .. ..$ intergenic_percentage : NULL
#> .. ..$ intergenic_frequency : NULL
#> .. ..$ promotercore_frequency : NULL
#> .. ..$ promotercore_percentage: NULL
#> .. ..$ fiveutr_frequency : NULL
#> .. ..$ fiveutr_percentage : NULL
#> .. ..$ threeutr_frequency : NULL
#> .. ..$ threeutr_percentage : NULL
#> .. ..$ promoterprox_frequency : NULL
#> .. ..$ promoterprox_percentage: NULL
#> ..$ sd :List of 18
#> .. ..$ number_of_regions : num 10188
#> .. ..$ gc_content : NULL
#> .. ..$ median_tss_dist : NULL
#> .. ..$ mean_region_width : num 170
#> .. ..$ exon_frequency : NULL
#> .. ..$ exon_percentage : NULL
#> .. ..$ intron_frequency : NULL
#> .. ..$ intron_percentage : NULL
#> .. ..$ intergenic_percentage : NULL
#> .. ..$ intergenic_frequency : NULL
#> .. ..$ promotercore_frequency : NULL
#> .. ..$ promotercore_percentage: NULL
#> .. ..$ fiveutr_frequency : NULL
#> .. ..$ fiveutr_percentage : NULL
#> .. ..$ threeutr_frequency : NULL
#> .. ..$ threeutr_percentage : NULL
#> .. ..$ promoterprox_frequency : NULL
#> .. ..$ promoterprox_percentage: NULL
#> $ plots :List of 1
#> ..$ region_commonality: NULL
#> $ description : chr "Data from [GEO GSE120532](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120532)\nGenome-wide maps of ch"| __truncated__
#> $ summary : NULL
#> $ bed_ids :List of 37
#> ..$ : chr "041fc0c13036b5b8d4c42d075ce943fa"
#> ..$ : chr "08c4e25d4a5320aa63b1ffbabb717d15"
#> ..$ : chr "1c34c33f029c5967b96b5bcd0bd25743"
#> ..$ : chr "1e43444e0f8071bf026b24cc55f1e86e"
#> ..$ : chr "2a9342b8b2648def09bc7156d1eeb1e6"
#> ..$ : chr "31a07e444fd57ec52d7da688038fbfd3"
#> ..$ : chr "3a881e4b1b0e3dc281a417703d387aed"
#> ..$ : chr "3af5bbcbd00e095809a511c5a60b6d45"
#> ..$ : chr "4eea36bcdfed04c1965cf513146a40e8"
#> ..$ : chr "4fcd2e45738ad83b0254e878520a497d"
#> ..$ : chr "54dbedb46409a93efbc774bc32cba1fe"
#> ..$ : chr "5535ea70b8d29830dd296613fe0128a1"
#> ..$ : chr "5fb9daa17b08f4d272751e814d3b94a6"
#> ..$ : chr "62d56a00d217962895f0823ce70b0548"
#> ..$ : chr "6d16b773ab23e63cc3bf23269faf5203"
#> ..$ : chr "6fe836d9a4e9257673e508bff3f9d91a"
#> ..$ : chr "843d4a57e79426df98697c964e7fbfc9"
#> ..$ : chr "8571b354e47013dd20e16063ab9eba17"
#> ..$ : chr "8daf787fb10ffa0c95b14597aa2a3a6e"
#> ..$ : chr "92f2c3a349c530c0f58957d3a76d78ee"
#> ..$ : chr "97087e835d3b08f04303d1c7aeba578b"
#> ..$ : chr "9c02b50af322fb2d46a1aa7f415c7eb3"
#> ..$ : chr "9cdc9a4d581062cbd34e7967032272bb"
#> ..$ : chr "9e8473aca735b5fd8efcab1a79cb0f59"
#> ..$ : chr "a7b45c97a5f48a717b714913968ab79d"
#> ..$ : chr "b7a11cf9634b67540703f76c454db941"
#> ..$ : chr "bac923f376af783db91ff869b4895a2a"
#> ..$ : chr "bc42426f303397cfcce9f1944681af8e"
#> ..$ : chr "bd9da8b4d0bdeefd1c90a3efbee5defb"
#> ..$ : chr "c851ceceb15a108ce1f3a0711a748450"
#> ..$ : chr "cc3b3e6b00f0d6f8dfce658d90543f2d"
#> ..$ : chr "d114c3b01e300a5d1c8f4fe0aaedd6b3"
#> ..$ : chr "d40e3212fac699679b1e6e60781b51c5"
#> ..$ : chr "deb5e6d83a15e97a84ed5c997b508c89"
#> ..$ : chr "e68be2f9de1d36d1df583a383bb56d51"
#> ..$ : chr "e9c69ef0359d1bf923c33802af6b4640"
#> ..$ : chr "ee9f86b809b086facd4bbb11f35d73f9"
#> $ author : chr "Jun, Huang"
#> $ source : chr "gse120532"