List files for ENCODE experiments — encode_list

Return file metadata for one or more ENCODE experiments. The table includes file accessions, formats, output types, assemblies, sizes, checksums, and download links. It does not download file contents.

Usage

encode_list_files(
  x,
  file_format = NULL,
  output_type = NULL,
  assembly = NULL,
  status = "released",
  limit = "all",
  metadata = c("basic", "full"),
  allow_many = FALSE,
  quiet = FALSE
)

Arguments

x: Experiment accession(s), experiment path(s), a search result from encode_search(), or a data frame containing experiment identifiers.
file_format: Optional file format filter, such as "fastq", "bed", "bigWig", or "tsv".
output_type: Optional ENCODE output type filter, such as "reads" or "gene quantifications".
assembly: Optional genome assembly filter, such as "GRCh38" or "mm10".
status: Optional file status filter. Use NULL to omit.
limit: Number of file records to request, or "all".
metadata: Amount of linked metadata to request. "basic" keeps responses smaller. "full" adds more display columns.
allow_many: Whether to allow many experiment datasets in one query.
quiet: If FALSE, print a concise status message.

Value

An encode_file_table data frame. Common columns include file_accession, experiment_accession, dataset_accession, file_format, output_type, assembly, file_size, md5sum, href, cloud_url, and parent experiment metadata when available. The function lists metadata only; it does not download file contents.

Details

The default limit = "all" requests the complete file list for the selected experiments.

Examples

files <- encode_list_files(
    "ENCSR523CTA",
    file_format = "tsv",
    output_type = "microRNA quantifications",
    assembly = "mm10",
    limit = 1,
    quiet = TRUE
)

encode_results(files)
#> ENCODE files
#> - files: 1
#> - experiments: 1
#> - known total size: 59.57 KB
#> Files:
#>         file  experiment        assay     organism format
#>  ENCFF838WBE ENCSR523CTA microRNA-seq Mus musculus    tsv
#>                    output assembly file_size   status
#>  microRNA quantifications     mm10  59.57 KB released