Display functions defined through the bedhost API and their corresponding parameters.
# S4 method for class 'BEDbase'
operations(x, ..., .deprecated = FALSE)list() API endpoints
bedbase <- BEDbase()
#> 125977 BED files available.
operations(bedbase)
#> $lending_page__get
#> lending_page__get
#> Lending Page
#>
#> Parameters:
#>
#> $index_v1_get
#> index_v1_get
#> API intro page
#> Description:
#> Display the index UI page
#>
#> Parameters:
#>
#> $embed_bed_file_v1_bed_embed_post
#> embed_bed_file_v1_bed_embed_post
#> Get embeddings for a bed file.
#> Description:
#> Create embedding for bed file
#>
#> Parameters:
#> file (string)
#>
#> $get_example_bed_record_v1_bed_example_get
#> get_example_bed_record_v1_bed_example_get
#> Get example BED record metadata
#> Description:
#> Get metadata for an example BED record.
#>
#> Parameters:
#>
#> $list_beds_v1_bed_list_get
#> list_beds_v1_bed_list_get
#> Paged list of all BED records
#> Description:
#> Returns list of BED files in the database with optional filters.
#>
#> Parameters:
#> limit (integer)
#> offset (integer)
#> genome (string)
#> filter by genome of the bed file. e.g. 'hg38'
#> bed_compliance (string)
#> filter by bed type. e.g. 'bed6+4'
#>
#> $missing_plots_v1_bed_missing_plots_get
#> missing_plots_v1_bed_missing_plots_get
#> Get missing plots for a bed file.
#> Description:
#> Get missing plots for a bed file
#>
#> example -> plot_id: gccontent
#>
#> Parameters:
#> plot_id (string)
#>
#> $bed_to_bed_search_v1_bed_search_bed_post
#> bed_to_bed_search_v1_bed_search_bed_post
#> Search for similar bed files
#>
#> Parameters:
#> limit (integer)
#> offset (integer)
#> file (string)
#>
#> $text_to_bed_search_v1_bed_search_text_post
#> text_to_bed_search_v1_bed_search_text_post
#> Search for a BedFile
#> Description:
#> Search for a BedFile by a text query.
#>
#> By default, it searches in the 'hg38' genome. To search in a
#> different genome, specify the `genome` parameter. eg. mm10 Example:
#> query="cancer"
#>
#> Parameters:
#> query (string)
#> genome ()
#> limit (integer)
#> offset (integer)
#>
#> $get_bed_embedding_v1_bed__bed_id__embedding_get
#> get_bed_embedding_v1_bed__bed_id__embedding_get
#> Get embeddings for a single BED record
#> Description:
#> Returns embeddings for a single BED record.
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_ref_gen_results_v1_bed__bed_id__genome_stats_get
#> get_ref_gen_results_v1_bed__bed_id__genome_stats_get
#> Get reference genome validation results
#> Description:
#> Return reference genome validation results for a bed file Example:
#> bed: 0dcdf8986a72a3d85805bbc9493a1302
#>
#> Parameters:
#> bed_id (string)
#>
#> $get_bed_metadata_v1_bed__bed_id__metadata_get
#> get_bed_metadata_v1_bed__bed_id__metadata_get
#> Get metadata for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#> full ()
#> Return full record with stats, plots, files and metadata
#>
#> $get_bed_classification_v1_bed__bed_id__metadata_classification_get
#> get_bed_classification_v1_bed__bed_id__metadata_classification_get
#> Get classification of single BED file
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_files_v1_bed__bed_id__metadata_files_get
#> get_bed_files_v1_bed__bed_id__metadata_files_get
#> Get metadata for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_plots_v1_bed__bed_id__metadata_plots_get
#> get_bed_plots_v1_bed__bed_id__metadata_plots_get
#> Get plots for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_pephub_v1_bed__bed_id__metadata_raw_get
#> get_bed_pephub_v1_bed__bed_id__metadata_raw_get
#> Get raw metadata for a single BED record
#> Description:
#> Returns raw metadata for a single BED record. This metadata is stored
#> in PEPHub. And is not verified.Example bed_id:
#> bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_stats_v1_bed__bed_id__metadata_stats_get
#> get_bed_stats_v1_bed__bed_id__metadata_stats_get
#> Get stats for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_neighbours_v1_bed__bed_id__neighbours_get
#> get_bed_neighbours_v1_bed__bed_id__neighbours_get
#> Get nearest neighbours for a single BED record
#> Description:
#> Returns most similar BED files in the database. Example bed_id:
#> bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#> limit (integer)
#> offset (integer)
#>
#> $get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get
#> get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get
#> Get regions from a BED file that overlap a query region.
#> Description:
#> Returns the queried regions with provided ID and optional query
#> parameters
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#> chr_num (string)
#> Chromosome number
#> start ()
#> query range: start coordinate
#> end ()
#> query range: start coordinate
#>
#> $get_tokens_v1_bed__bed_id__tokens__universe_id__get
#> get_tokens_v1_bed__bed_id__tokens__universe_id__get
#> Get tokenized of bed file
#> Description:
#> Return univers of bed file Example: bed:
#> 0dcdf8986a72a3d85805bbc9493a1302 | universe:
#> 58dee1672b7e581c8e1312bd4ca6b3c7
#>
#> Parameters:
#> bed_id (string)
#> universe_id (string)
#>
#> $get_tokens_v1_bed__bed_id__tokens__universe_id__info_get
#> get_tokens_v1_bed__bed_id__tokens__universe_id__info_get
#> Get link to tokenized bed file
#> Description:
#> Return link to tokenized bed file Example: bed:
#> 0dcdf8986a72a3d85805bbc9493a1302 | universe:
#> 58dee1672b7e581c8e1312bd4ca6b3c7
#>
#> Parameters:
#> bed_id (string)
#> universe_id (string)
#>
#> $create_bedset_v1_bedset_create_post
#> create_bedset_v1_bedset_create_post
#> Create Bedset
#> Description:
#> Create a new bedset by providing registry path to the PEPhub project
#>
#> Parameters:
#> registry_path (string)
#>
#> $get_example_bedset_record_v1_bedset_example_get
#> get_example_bedset_record_v1_bedset_example_get
#> Get metadata for an example BEDset record
#>
#> Parameters:
#>
#> $list_bedsets_v1_bedset_list_get
#> list_bedsets_v1_bedset_list_get
#> Paged list of all BEDset records
#> Description:
#> Returns a list of BEDset records in the database with optional
#> filters and search.
#>
#> Parameters:
#> query (string)
#> limit (integer)
#> offset (integer)
#>
#> $get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get
#> get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get
#> Get Bedfiles In Bedset
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_bedset_metadata_v1_bedset__bedset_id__metadata_get
#> get_bedset_metadata_v1_bedset__bedset_id__metadata_get
#> Get all metadata for a single BEDset record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#> full (boolean)
#>
#> $get_bedset_metadata_v1_bedset__bedset_id__metadata_plots_get
#> get_bedset_metadata_v1_bedset__bedset_id__metadata_plots_get
#> Get plots for single bedset record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_bedset_metadata_v1_bedset__bedset_id__metadata_stats_get
#> get_bedset_metadata_v1_bedset__bedset_id__metadata_stats_get
#> Get stats for a single BEDSET record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_bedset_pep_v1_bedset__bedset_id__pep_get
#> get_bedset_pep_v1_bedset__bedset_id__pep_get
#> Download PEP project for a single BEDset record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get
#> get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get
#> Get Track Hub Bedset
#> Description:
#> Generate track hub files for the BED set
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head
#> get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head
#> Get Track Hub Bedset
#> Description:
#> Generate track hub files for the BED set
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_detailed_stats_v1_detailed_stats_get
#> get_detailed_stats_v1_detailed_stats_get
#> Get detailed statistics for BEDbase platform, including number of files for each genome
#> Description:
#> Returns detailed statistics
#>
#> Parameters:
#> concise (boolean)
#>
#> $get_detailed_usage_v1_detailed_usage_get
#> get_detailed_usage_v1_detailed_usage_get
#> Get detailed usage statistics for BEDbase platform
#> Description:
#> Returns detailed usage statistics
#>
#> Parameters:
#>
#> $changelog_v1_docs_changelog_get
#> changelog_v1_docs_changelog_get
#> Release notes
#>
#> Parameters:
#>
#> $redirect_to_download_v1_files__file_path__get
#> redirect_to_download_v1_files__file_path__get
#> Redirect To Download
#>
#> Parameters:
#> file_path (string)
#>
#> $get_bedbase_db_stats_v1_genomes_get
#> get_bedbase_db_stats_v1_genomes_get
#> Get available genomes
#> Description:
#> Returns statistics
#>
#> Parameters:
#>
#> $get_drs_object_metadata_v1_objects__object_id__get
#> get_drs_object_metadata_v1_objects__object_id__get
#> Get DRS object metadata
#> Description:
#> Returns metadata about a DrsObject.
#>
#> Parameters:
#> object_id (string)
#>
#> $get_object_bytes_url_v1_objects__object_id__access__access_id__get
#> get_object_bytes_url_v1_objects__object_id__access__access_id__get
#> Get URL where you can retrieve files
#> Description:
#> Returns a URL that can be used to fetch the bytes of a DrsObject.
#>
#> Parameters:
#> object_id (string)
#> access_id (string)
#>
#> $get_object_bytes_v1_objects__object_id__access__access_id__bytes_get
#> get_object_bytes_v1_objects__object_id__access__access_id__bytes_get
#> Download actual file
#> Description:
#> Returns the bytes of a DrsObject.
#>
#> Parameters:
#> object_id (string)
#> access_id (string)
#>
#> $get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get
#> get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get
#> Download thumbnail file
#> Description:
#> Returns the bytes of a thumbnail of a DrsObject
#>
#> Parameters:
#> object_id (string)
#> access_id (string)
#>
#> $service_info_v1_service_info_get
#> service_info_v1_service_info_get
#> GA4GH service info
#> Description:
#> Returns information about this service, such as versions, name, etc.
#>
#> Parameters:
#>
#> $get_bedbase_db_stats_v1_stats_get
#> get_bedbase_db_stats_v1_stats_get
#> Get summary statistics for BEDbase platform
#> Description:
#> Returns statistics
#>
#> Parameters:
#>