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()
#> 128999 BED files available.
ex_bed <- bb_example(bedbase, "bed")
str(ex_bed)
#> List of 22
#> $ name : chr "Histone ChIP-seq from SJSA1 (ENCLB902REK)"
#> $ genome_alias : chr "hg38"
#> $ genome_digest : NULL
#> $ bed_compliance : chr "bed6+4"
#> $ data_format : chr "encode_narrowpeak"
#> $ compliant_columns : int 6
#> $ non_compliant_columns: int 4
#> $ header : NULL
#> $ id : chr "e3fb49d8d0b292d51e0bca8b021357ad"
#> $ description : chr "H3K27me3 ChIP-seq on human SJSA1"
#> $ submission_date : chr "2025-06-03T19:53:38.941093Z"
#> $ last_update_date : chr "2025-08-29T20:12:17.721073Z"
#> $ 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 ""
#> ..$ tissue : chr ""
#> ..$ library_source : chr "genomic"
#> ..$ assay : chr "ChIP-Seq"
#> ..$ antibody : chr "H3K27me3"
#> ..$ target : chr ""
#> ..$ treatment : chr ""
#> ..$ global_sample_id :List of 1
#> .. ..$ : chr "geo:gsm5111821"
#> ..$ global_experiment_id:List of 1
#> .. ..$ : chr "geo:gse167669"
#> ..$ original_file_name : chr "GSM5111821_ENCFF117KAW_pseudoreplicated_peaks_GRCh38.bed.gz"
#> $ processed : logi FALSE
#> $ 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 "gse197519"
#> $ name : chr "gse197519"
#> $ md5sum : chr "68446c42cb23bce7207f3b6f4a761387"
#> $ submission_date : chr "2025-05-02T10:19:51.283823Z"
#> $ last_update_date: chr "2025-05-02T10:19:51.283826Z"
#> $ statistics :List of 2
#> ..$ mean:List of 18
#> .. ..$ number_of_regions : NULL
#> .. ..$ gc_content : NULL
#> .. ..$ median_tss_dist : NULL
#> .. ..$ mean_region_width : NULL
#> .. ..$ 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 : NULL
#> .. ..$ gc_content : NULL
#> .. ..$ median_tss_dist : NULL
#> .. ..$ mean_region_width : NULL
#> .. ..$ 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 GSE197519](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197519)\nVanguard is a glucose "| __truncated__
#> $ summary : NULL
#> $ bed_ids :List of 2
#> ..$ : chr "3053b7b8be8ca1502b46946dde0e4ced"
#> ..$ : chr "98d8fbbdde4e7b510e4b5f9fe469b78f"
#> $ author : chr "Ben, Zhang"
#> $ source : chr "gse197519"