Search metadata: AnnotationHub — search_annotationhub • PeakyFinders

Search metadata from AnnotationHub.

search_annotationhub(
  searches = construct_searches(),
  ah_id = NULL,
  output_category = NULL,
  output_type = NULL,
  file_format_type = NULL,
  biosample_id = NULL,
  biosample_type = NULL,
  biosample_name = NULL,
  dataset_biosample_summary = NULL,
  dataprovider = NULL,
  species = NULL,
  genome = NULL,
  description = NULL,
  rdataclass = NULL,
  sourcetype = NULL,
  partial_match = TRUE,
  peaks_only = FALSE,
  verbose = TRUE,
  ...
)

Source

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

Arguments

searches: Named list of regex queries.
ah_id: Search "ah_id" column.
output_category: Search "output_category" column.
output_type: Search "output_type" column.
file_format_type: Search "file_format_type" column.
biosample_id: Search "biosample_id" column.
biosample_type: Search "biosample_type" column.
biosample_name: Search "biosample_name" column.
dataset_biosample_summary: Search "dataset_biosample_summary" column.
dataprovider: Search "dataprovider" column.
species: Search "species" column.
genome: Search "genome" column.
description: Search "description" column.
rdataclass: Search "rdataclass" column.
sourcetype: Search "sourcetype" 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_annotationhub(searches=construct_searches(keys="narrowpeak"),
                             biosample_type="brain",
                             peaks_only=TRUE)
#> Subsetting metadata to only peaks.
#> Returning filtered metadata: 12,483 entries.