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()
#> 125977 BED files available.

ex_bed <- bb_example(bedbase, "bed")
bb_metadata(bedbase, ex_bed$id)
#> $name
#> [1] "encode_10240"
#> 
#> $genome_alias
#> [1] "hg38"
#> 
#> $genome_digest
#> [1] "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
#> 
#> $bed_compliance
#> [1] "bed6+3"
#> 
#> $data_format
#> [1] "encode_broadpeak"
#> 
#> $compliant_columns
#> [1] 6
#> 
#> $non_compliant_columns
#> [1] 3
#> 
#> $header
#> NULL
#> 
#> $id
#> [1] "afbdec2bd8ff7f22467a39d6146d1714"
#> 
#> $description
#> [1] "GM DNase-seq experiment on K562 (Blast phase chronic myelogenous leukemia, BCR-ABL1 positive cell line from pleural effusion)"
#> 
#> $submission_date
#> [1] "2025-04-28T23:15:53.132875Z"
#> 
#> $last_update_date
#> [1] "2025-07-18T20:52:00.968951Z"
#> 
#> $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] ""
#> 
#> $annotation$cell_line
#> [1] "K562"
#> 
#> $annotation$tissue
#> [1] ""
#> 
#> $annotation$library_source
#> [1] "genomic"
#> 
#> $annotation$assay
#> [1] "DNase-Hypersensitivity"
#> 
#> $annotation$antibody
#> [1] ""
#> 
#> $annotation$target
#> [1] ""
#> 
#> $annotation$treatment
#> [1] ""
#> 
#> $annotation$global_sample_id
#> $annotation$global_sample_id[[1]]
#> [1] "encode:ENCFF708QSW"
#> 
#> $annotation$global_sample_id[[2]]
#> [1] "geo:gsm2400267"
#> 
#> 
#> $annotation$global_experiment_id
#> $annotation$global_experiment_id[[1]]
#> [1] "encode"
#> 
#> $annotation$global_experiment_id[[2]]
#> [1] "geo:gse90287"
#> 
#> 
#> $annotation$original_file_name
#> [1] "GSM2400267_ENCFF708QSW_hotspots_GRCh38.bed.gz"
#> 
#> 
#> $processed
#> [1] TRUE
#> 
#> $stats
#> NULL
#> 
#> $plots
#> NULL
#> 
#> $files
#> NULL
#> 
#> $universe_metadata
#> NULL
#> 
#> $raw_metadata
#> NULL
#> 
#> $bedsets
#> list()
#> 

ex_bedset <- bb_example(bedbase, "bedset")
bb_metadata(bedbase, ex_bedset$id)
#> $id
#> [1] "gse127704"
#> 
#> $name
#> [1] "gse127704"
#> 
#> $md5sum
#> [1] "b509b959846303ecba35adc66e7838ff"
#> 
#> $submission_date
#> [1] "2025-06-03T16:17:24.565586Z"
#> 
#> $last_update_date
#> [1] "2025-06-03T16:17:24.565590Z"
#> 
#> $statistics
#> NULL
#> 
#> $plots
#> NULL
#> 
#> $description
#> [1] "Data from [GEO GSE127704](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127704)\nChIP-seq from K562 (ENCSR497VFH)"
#> 
#> $summary
#> NULL
#> 
#> $bed_ids
#> $bed_ids[[1]]
#> [1] "3b56d2689a821ef80da854e789e7c4bc"
#> 
#> $bed_ids[[2]]
#> [1] "4704124ec926afd6c557536f3ddd266a"
#> 
#> $bed_ids[[3]]
#> [1] "58114a3e44dea03decaa305f35c0f60b"
#> 
#> $bed_ids[[4]]
#> [1] "9a2adba03018d2e8780fb743a7d7dc3c"
#> 
#> 
#> $author
#> [1] "ENCODE, DCC"
#> 
#> $source
#> [1] "gse127704"
#>