Get metadata for a BED file or BEDset

Get metadata for a BED file or BEDset given its id. Abort if not found or id is not not 32 characters.

bb_metadata(bedbase, id, full = FALSE)

Arguments

bedbase

BEDbase() object

id

integer(1) record or object identifier

full

logical(1) (default FALSE) include full record with stats, files, and metadata

Value

list() metadata

Examples

bedbase <- BEDbase()
#> 663721 BED files available.

ex_bed <- bb_example(bedbase, "bed")
bb_metadata(bedbase, ex_bed$id)
#> $name
#> [1] "ENCFF370XZK"
#> 
#> $genome_alias
#> [1] "hg38"
#> 
#> $genome_digest
#> [1] "Ba88PY52_qeifhJrgUXyin6UITdXNsg3"
#> 
#> $bed_compliance
#> [1] "bed5+1"
#> 
#> $data_format
#> [1] "bed_like_rs"
#> 
#> $compliant_columns
#> [1] 5
#> 
#> $non_compliant_columns
#> [1] 1
#> 
#> $header
#> NULL
#> 
#> $id
#> [1] "0000143becc12fcd50c62f3d78fe7421"
#> 
#> $description
#> [1] "female adult (53 years)"
#> 
#> $submission_date
#> [1] "2026-04-09T19:40:03.413783Z"
#> 
#> $last_update_date
#> [1] "2026-04-14T18:46:25.972343Z"
#> 
#> $is_universe
#> [1] FALSE
#> 
#> $license_id
#> [1] "DUO:0000042"
#> 
#> $annotation
#> $annotation$species_name
#> [1] "Homo sapiens"
#> 
#> $annotation$species_id
#> [1] "9606"
#> 
#> $annotation$genotype
#> [1] ""
#> 
#> $annotation$phenotype
#> [1] ""
#> 
#> $annotation$description
#> [1] ""
#> 
#> $annotation$cell_type
#> [1] "adrenal gland"
#> 
#> $annotation$cell_line
#> NULL
#> 
#> $annotation$tissue
#> [1] "endocrine gland, adrenal gland"
#> 
#> $annotation$library_source
#> NULL
#> 
#> $annotation$assay
#> [1] "PRO-cap"
#> 
#> $annotation$antibody
#> NULL
#> 
#> $annotation$target
#> NULL
#> 
#> $annotation$treatment
#> NULL
#> 
#> $annotation$global_sample_id
#> $annotation$global_sample_id[[1]]
#> [1] "encode:ENCFF370XZK"
#> 
#> 
#> $annotation$global_experiment_id
#> $annotation$global_experiment_id[[1]]
#> [1] "encode:ENCSR970ACM"
#> 
#> 
#> $annotation$original_file_name
#> [1] "ENCFF370XZK.bed.gz"
#> 
#> 
#> $processed
#> [1] FALSE
#> 
#> $stats
#> NULL
#> 
#> $plots
#> NULL
#> 
#> $files
#> NULL
#> 
#> $universe_metadata
#> NULL
#> 
#> $bedsets
#> list()
#> 

ex_bedset <- bb_example(bedbase, "bedset")
bb_metadata(bedbase, ex_bedset$id)
#> $id
#> [1] "gse215730"
#> 
#> $name
#> [1] "gse215730"
#> 
#> $md5sum
#> [1] "cae5279e7f5968da1c336a582a222646"
#> 
#> $submission_date
#> [1] "2025-06-03T01:45:11.656025Z"
#> 
#> $last_update_date
#> [1] "2025-06-03T01:45:11.656029Z"
#> 
#> $statistics
#> NULL
#> 
#> $distributions
#> NULL
#> 
#> $plots
#> NULL
#> 
#> $description
#> [1] "Data from [GEO GSE215730](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215730)\nDNase-seq from layer of hippocampus (ENCSR385DQL)"
#> 
#> $summary
#> NULL
#> 
#> $bed_ids
#> $bed_ids[[1]]
#> [1] "304c5d3c640fa4e7c8eff776d949b094"
#> 
#> $bed_ids[[2]]
#> [1] "373911a60adc78187c9459078568addf"
#> 
#> $bed_ids[[3]]
#> [1] "7b698bb0bffd9e017dc66c5fb8de282e"
#> 
#> $bed_ids[[4]]
#> [1] "7e676e9600264056f7130cce5b0819ed"
#> 
#> $bed_ids[[5]]
#> [1] "9a44280d2faa47d8080504761ec92c9c"
#> 
#> $bed_ids[[6]]
#> [1] "ce91ca909578975df44ac5eba0d9e2ae"
#> 
#> 
#> $bedfile_count
#> [1] 6
#> 
#> $author
#> [1] "ENCODE, DCC"
#> 
#> $source
#> [1] "gse215730"
#>