Search metadata: ENCODE — search_encode • PeakyFinders

Search metadata from the Encyclopedia of DNA Elements (ENCODE).

search_encode(
  assay = NULL,
  accession = NULL,
  file_accession = NULL,
  file_type = NULL,
  file_format = NULL,
  output_category = NULL,
  biosample_id = NULL,
  biosample_type = NULL,
  biosample_name = NULL,
  organism = NULL,
  dataset_type = NULL,
  assembly = NULL,
  genome_annotation = NULL,
  partial_match = TRUE,
  peaks_only = FALSE,
  verbose = TRUE,
  ...
)

Source

https://github.com/neurogenomics/EpiCompare/issues/43 Discussion on EpiCompare GitHub.

https://biodatascience.github.io/compbio/bioc/anno.html Mike Love tutorial on accessing peak data from AnnotationHub.

Arguments

assay: Search "assay" column.
accession: Search "accession" column.
file_accession: Search "file_accession" column.
file_type: Search "file_type" column.
file_format: Search "file_format" column.
output_category: Search "output_category" column.
biosample_id: Search "biosample_id" column.
biosample_type: Search "biosample_type" column.
biosample_name: Search "biosample_name" column.
organism: Search "organism" column.
dataset_type: Search "dataset_type" column.
assembly: Search "assembly" column.
genome_annotation: Search "genome_annotation" column.
partial_match: Return case-insensitive substring matches instead of exact matches only (default: TRUE).
peaks_only: Return pre-filtered metadata for peak data aligned to the GRCh38 human genome build.
verbose: Print messages.
...: Additional metadata columns to filter.

Value

data.table.

Examples

meta <- search_encode(assay = "chip-seq", 
                      biosample_name = "K562",
                      file_type = "peak",
                      assembly = "GRCh38",
                      organism = "Homo sapiens",
                      partial_match = TRUE)
#> Importing metadata via AnnotationHub.
#> snapshotDate(): 2022-05-13
#> loading from cache
#> Filtering by: assay
#> Filtering by: file_type
#> Filtering by: biosample_name
#> Filtering by: organism
#> Filtering by: assembly
#> Returning filtered metadata: 4,978 entries.