Select ENCODE files to use or download — encode_select

Choose files from an encode_list_files() table using explicit filters or a preset. The result keeps the selected files for download or reading.

Usage

encode_select_files(
  files,
  preset = NULL,
  file_format = NULL,
  output_type = NULL,
  assembly = NULL,
  file_accession = NULL,
  status = "released",
  replicate_policy = c("all", "preferred_processed", "replicate_level", "pooled_only"),
  prefer_default = FALSE,
  require_href = TRUE,
  quiet = FALSE
)

Arguments

files: File metadata from encode_list_files(), a File search result, a selected-file object, or ENCFF accession(s).
preset: Optional preset name. Use encode_file_presets() to list the canonical preset names.
file_format: Optional file format filter. If omitted and preset is set, the preset supplies a format preference.
output_type: Optional output type filter. If omitted and preset is set, the preset supplies an output-type priority.
assembly: Optional genome assembly filter.
file_accession: Optional ENCODE file accession(s), such as "ENCFF260OJQ", to select explicitly before applying other filters.
status: Optional status filter. Defaults to "released".
replicate_policy: How to handle replicate-related outputs. "all" keeps all matching files; "preferred_processed" keeps the highest-priority output type per experiment when a preset priority is available; "replicate_level" keeps files with biological replicate labels; "pooled_only" keeps files whose output type indicates pooled or IDR-like processing.
prefer_default: Whether to prefer ENCODE records marked preferred_default. When no preferred-default rows are present, the filter is skipped and the other explicit criteria are used.
require_href: Whether selected rows must include an ENCODE download path or URL.
quiet: If FALSE, print a concise selection message.

Value

An encode_selected_files object with files, the selected encode_file_table; excluded, a table of non-selected rows and reasons; criteria, the applied filters and preset settings; query_url; and retrieved_at.

Details

Use encode_file_presets() to list available presets or inspect one preset.

Examples

files <- data.frame(
    file_accession = c("ENCFFONE", "ENCFFTWO"),
    file_format = c("tsv", "bed"),
    output_type = c("gene quantifications", "peaks"),
    assembly = "mm10",
    status = "released",
    href = c(
        "/files/ENCFFONE/@@download/a.tsv",
        "/files/ENCFFTWO/@@download/b.bed"
    )
)

selected <- encode_select_files(
    files,
    preset = "rnaseq_gene_quant",
    assembly = "mm10",
    quiet = TRUE
)

encode_results(selected)
#> ENCODE files
#> - files: 1
#> - experiments: 0
#> Files:
#>      file format               output assembly   status
#>  ENCFFONE    tsv gene quantifications     mm10 released