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()
#> 130451 BED files available.
ex_bed <- bb_example(bedbase, "bed")
str(ex_bed)
#> List of 22
#> $ name : chr "M1_24hrs_Rep1_bATACseq"
#> $ genome_alias : chr "hg38"
#> $ genome_digest : NULL
#> $ bed_compliance : chr "bed3+0"
#> $ data_format : chr "ucsc_bed"
#> $ compliant_columns : int 3
#> $ non_compliant_columns: int 0
#> $ header : NULL
#> $ id : chr "f07ff93f4d1389116b42cfa515aa3b6a"
#> $ description : chr "M1_24hrs_bATACseq_IDRoutput.bed.gz"
#> $ submission_date : chr "2025-06-03T20:32:47.156191Z"
#> $ last_update_date : chr "2025-12-23T00:10:09.651402Z"
#> $ 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 "M1"
#> ..$ cell_line : chr ""
#> ..$ tissue : chr ""
#> ..$ library_source : chr "genomic"
#> ..$ assay : chr "ATAC-seq"
#> ..$ antibody : chr ""
#> ..$ target : chr ""
#> ..$ treatment : chr "Differentiation of HL-60 cells into M0 macrophages (Murao et al., 1983). Aditionally, M0 cells were polarized i"| __truncated__
#> ..$ global_sample_id :List of 1
#> .. ..$ : chr "geo:gsm5012252"
#> ..$ global_experiment_id:List of 1
#> .. ..$ : chr "geo:gse164498"
#> ..$ original_file_name : chr "GSM5012252_M1_24hrs_Rep1_bATACseq_HomerPeaks.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 "gse125061"
#> $ name : chr "gse125061"
#> $ md5sum : chr "6dcc9a18dc9965cfc14abe7fa39d478c"
#> $ submission_date : chr "2025-05-23T12:16:22.281419Z"
#> $ last_update_date: chr "2025-05-23T12:16:22.281424Z"
#> $ statistics :List of 2
#> ..$ mean:List of 18
#> .. ..$ number_of_regions : num 22557
#> .. ..$ gc_content : NULL
#> .. ..$ median_tss_dist : NULL
#> .. ..$ mean_region_width : num 153
#> .. ..$ 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 963
#> .. ..$ gc_content : NULL
#> .. ..$ median_tss_dist : NULL
#> .. ..$ mean_region_width : num 3.2
#> .. ..$ 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 GSE125061](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125061)\nThe transition from qu"| __truncated__
#> $ summary : NULL
#> $ bed_ids :List of 2
#> ..$ : chr "0692dfe199d26353af23dcbf354a6548"
#> ..$ : chr "36baa7aead2bad3062342fafad6c7197"
#> $ author : chr "Alexander, James, Murison"
#> $ source : chr "gse125061"