An R client for BEDbase

bedbaser exposes the bedhost API and includes convenience functions for common tasks, such as to import a BED file by id into a GRanges object and a BEDset by its id into a GRangesList.

BEDbase(cache_path, quietly = FALSE)

getCache(x, cache_type = c("bedfiles", "bedsets"))

setCache(x, cache_path, quietly = TRUE)

Arguments

cache_path

character(1)

quietly

logical(1) (default TRUE) display messages

x

BEDbase() object

cache_type

character(1) bedfiles or bedsets

Value

BEDbase object

Details

BEDbase() creates a cache similar to that of the Geniml BBClient's cache.

The convenience functions are as follows

• bedbaser::BEDbase(): API service constructor

• bedbaser::getCache(): Retrieve cache

• bedbaser::setCache(): Set path to cache

• bedbaser::bb_stats(): Retrieve BEDbase statistics

• bedbaser::bb_example(): Retrieve an example BED file or BEDset

• bedbaser::bb_metadata(): Retrieve metadata for a BED file or BEDset

• bedbaser::bb_list_beds(): List all BED files

• bedbaser::bb_list_bedsets(): List all BEDsets

• bedbaser::bb_beds_in_bedset(): List BED files in BEDset

• bedbaser::bb_bed_text_search(): Search BED files by text

• bedbaser::bb_to_granges(): Create a GRanges object from a BED id

• bedbaser::bb_to_grangeslist(): Create a GRangesList from a BEDset id

• bedbaser::bb_save(): Save a BED file to a path.

Examples

bedbase <- BEDbase(cache_path = tempdir())
#> 130451 BED files available.
ex_bed <- bb_example(bedbase, "bed")
bb_metadata(bedbase, ex_bed$id)
#> $name
#> [1] "M1_24hrs_Rep1_bATACseq"
#> 
#> $genome_alias
#> [1] "hg38"
#> 
#> $genome_digest
#> NULL
#> 
#> $bed_compliance
#> [1] "bed3+0"
#> 
#> $data_format
#> [1] "ucsc_bed"
#> 
#> $compliant_columns
#> [1] 3
#> 
#> $non_compliant_columns
#> [1] 0
#> 
#> $header
#> NULL
#> 
#> $id
#> [1] "f07ff93f4d1389116b42cfa515aa3b6a"
#> 
#> $description
#> [1] "M1_24hrs_bATACseq_IDRoutput.bed.gz"
#> 
#> $submission_date
#> [1] "2025-06-03T20:32:47.156191Z"
#> 
#> $last_update_date
#> [1] "2025-12-23T00:10:09.651402Z"
#> 
#> $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] "M1"
#> 
#> $annotation$cell_line
#> [1] ""
#> 
#> $annotation$tissue
#> [1] ""
#> 
#> $annotation$library_source
#> [1] "genomic"
#> 
#> $annotation$assay
#> [1] "ATAC-seq"
#> 
#> $annotation$antibody
#> [1] ""
#> 
#> $annotation$target
#> [1] ""
#> 
#> $annotation$treatment
#> [1] "Differentiation of HL-60 cells into M0 macrophages (Murao et al., 1983). Aditionally, M0 cells were polarized into M1 and M2 macrophages (Huang et al., 2018) as previously described. Lastly, M2 cells were repolarized towards M1., Differentiation of HL-60 cells into M0 macrophages was performed as described (Murao et al., 1983). Aditionally, M0 cells were polarized into M1 and M2 macrophages (Huang et al., 2018) as previously described. Lastly, M2 cells were repolarized towards M1."
#> 
#> $annotation$global_sample_id
#> $annotation$global_sample_id[[1]]
#> [1] "geo:gsm5012252"
#> 
#> 
#> $annotation$global_experiment_id
#> $annotation$global_experiment_id[[1]]
#> [1] "geo:gse164498"
#> 
#> 
#> $annotation$original_file_name
#> [1] "GSM5012252_M1_24hrs_Rep1_bATACseq_HomerPeaks.bed.gz"
#> 
#> 
#> $processed
#> [1] FALSE
#> 
#> $stats
#> NULL
#> 
#> $plots
#> NULL
#> 
#> $files
#> NULL
#> 
#> $universe_metadata
#> NULL
#> 
#> $raw_metadata
#> NULL
#> 
#> $bedsets
#> list()
#>