zenodo_download {OmnipathR} | R Documentation

## 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'
    )

[Package OmnipathR version 3.2.0 Index]