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Complete list of all experiments in refine.bio

Source: R/get_experiment_catalog.R
get_experiment_catalog.Rd

Refine.bio experiments are collections of samples that were processed together. In practices, refine.bio experiments are usually a GEO series or an SRA study. This function returns a list of all experiments in refine.bio as a tibble.

Usage

get_experiment_catalog(.pages = 1e+05)

Arguments

.pages

integer(1) The number of pages to retrieve (with default=Inf). Generally, you'll want to ignore this; it's only useful for testing.

Value

tibble A tibble of all experiments in refine.bio.

The tibble contains the following columns:

  • id: The ID of the experiment

  • title: The title of the experiment

  • publication_title: The title of the publication associated with the experiment

  • description: A description of the experiment

  • accession_code: The accession code of the experiment

  • alternate_accession_code: An alternate accession code for the experiment

  • technology: The technology used to generate the data in the experiment

  • submitter_institution: The institution that submitted the experiment

  • has_publication: Whether the experiment has a publication associated with it

  • publication_doi: The DOI of the publication associated with the experiment

  • publication_authors: The authors of the publication associated with the experiment

  • pubmed_id: The PubMed ID of the publication associated with the experiment

  • source_first_published: The date the experiment was first published

  • num_total_samples: The total number of samples in the experiment

  • num_processed_samples: The number of samples in the experiment that have been processed

  • num_downloadable_samples: The number of samples in the experiment that are downloadable

  • platform_names: The names of the platforms used in the experiment

  • organism_names: The names of the organisms in the experiment

  • sample_metadata_fields: The types of metadata available for the samples in the experiment

  • samples: a data.frame of sample metadata

Author

Examples

# this takes about 1-2 minutes to complete
# for the entire experiment listing
# depending on your internet connection
# You only need to do this once (or when you want
#   to update the results)

# get the first 2 pages of experiments for
# testing and demonstration purposes
experiments <- experiment_listing(.pages = 2)
#> Error in experiment_listing(.pages = 2): could not find function "experiment_listing"

# get all experiments
# experiments <- get_experiment_catalog()

head(experiments)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'head': object 'experiments' not found
dim(experiments)
#> Error: object 'experiments' not found
colnames(experiments)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colnames': object 'experiments' not found