zenodo_download: Retrieves data from Zenodo

In saezlab/OmnipathR: OmniPath web service client and more

Retrieves data from Zenodo

Description

Zenodo is a repository of large scientific datasets. Many projects and publications make their datasets available at Zenodo. This function downloads an archive from Zenodo and extracts the requested file.

Usage

zenodo_download(
  path,
  reader = NULL,
  reader_param = list(),
  url_key = NULL,
  zenodo_record = NULL,
  zenodo_fname = NULL,
  url_param = list(),
  url_key_param = list(),
  ...
)

Arguments

path	Character: path to the file within the archive.
reader	Optional, a function to read the connection.
reader_param	List: arguments for the reader function.
url_key	Character: name of the option containing the URL
zenodo_record	The Zenodo record ID, either integer or character.
zenodo_fname	The file name within the record.
url_param	List: variables to insert into the URL string (which is returned from the options).
url_key_param	List: variables to insert into the 'url_key'.
...	Passed to archive_extractor

Value

A connection

Examples

# an example from the OmnipathR::remap_tf_target_download function:
remap_dorothea <- zenodo_download(
    zenodo_record = 3713238,
    zenodo_fname = 'tf_target_sources.zip',
    path = (
        'tf_target_sources/chip_seq/remap/gene_tf_pairs_genesymbol.txt'
    ),
    reader = read_tsv,
    reader_param = list(
        col_names = c(
            'source_genesymbol',
            'target_genesymbol',
            'target_ensembl',
            'score'
        ),
        col_types = cols(),
        progress = FALSE
    ),
  resource = 'ReMap'
)

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.