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()
#> 168208 BED files available.

ex_bed <- bb_example(bedbase, "bed")
bb_metadata(bedbase, ex_bed$id)
#> $name
#> [1] "encode_2074"
#> 
#> $genome_alias
#> [1] "hg38"
#> 
#> $genome_digest
#> [1] "Ba88PY52_qeifhJrgUXyin6UITdXNsg3"
#> 
#> $bed_compliance
#> [1] "bed6+3"
#> 
#> $data_format
#> [1] "encode_broadpeak"
#> 
#> $compliant_columns
#> [1] 6
#> 
#> $non_compliant_columns
#> [1] 3
#> 
#> $header
#> NULL
#> 
#> $id
#> [1] "ee0c316f02b443c27b0136cb85c113c5"
#> 
#> $description
#> [1] "DNase-seq experiment on SJSA1 (Osteosarcoma cell line from femur)"
#> 
#> $submission_date
#> [1] "2025-04-24T23:25:31.252448Z"
#> 
#> $last_update_date
#> [1] "2026-02-08T09:56:25.908938Z"
#> 
#> $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] "SJSA1"
#> 
#> $annotation$tissue
#> [1] ""
#> 
#> $annotation$library_source
#> [1] ""
#> 
#> $annotation$assay
#> [1] "DNase-seq"
#> 
#> $annotation$antibody
#> [1] ""
#> 
#> $annotation$target
#> [1] ""
#> 
#> $annotation$treatment
#> [1] ""
#> 
#> $annotation$global_sample_id
#> $annotation$global_sample_id[[1]]
#> [1] "encode:ENCFF209ZHV"
#> 
#> 
#> $annotation$global_experiment_id
#> $annotation$global_experiment_id[[1]]
#> [1] "encode"
#> 
#> 
#> $annotation$original_file_name
#> [1] "ENCFF209ZHV.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] "gse96780"
#> 
#> $name
#> [1] "gse96780"
#> 
#> $md5sum
#> [1] "ad1c44fa4dfd062170149d4c60dae901"
#> 
#> $submission_date
#> [1] "2026-02-09T12:03:04.490935Z"
#> 
#> $last_update_date
#> [1] "2026-02-09T12:03:04.490938Z"
#> 
#> $statistics
#> NULL
#> 
#> $plots
#> NULL
#> 
#> $description
#> [1] "Data from [GEO GSE96780](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96780)\nGenome-wide maps of histone H3K27 acetylation in A549 and MSR-A549 cells."
#> 
#> $summary
#> NULL
#> 
#> $bed_ids
#> $bed_ids[[1]]
#> [1] "843d6c4fafb7d1ddeab7fc752fc9d7e2"
#> 
#> $bed_ids[[2]]
#> [1] "bfffc80ce10af0e3e1a8ed7727f254a8"
#> 
#> 
#> $author
#> [1] "Hideo, Watanabe"
#> 
#> $source
#> [1] "gse96780"
#>