download_bigg_universal_metabolite: Download BiGG Universal Metabolite Data

In tidymass/massdatabase: Play with databases about mass spectrometry

Download BiGG Universal Metabolite Data

Description

This function downloads the BiGG universal metabolite database, saving it to a specified directory. It provides the option to store intermediate files and control the download rate by introducing a delay.

Usage

download_bigg_universal_metabolite(
  path = ".",
  sleep = 1,
  delete_intermediate = TRUE
)

Arguments

path	A string specifying the directory to save the downloaded data. Defaults to the current directory ('"."').
sleep	A numeric value indicating the number of seconds to pause between downloads. Defaults to 1 second.
delete_intermediate	A logical value indicating whether to delete intermediate files after the download completes. Defaults to 'TRUE'.

Details

The function first retrieves a list of all available metabolites from the BiGG database using 'request_bigg_universal_metabolite_info()'. It saves this information in an intermediate directory. For each metabolite, the function checks if the data already exists locally; if not, it downloads the data using 'request_bigg_universal_metabolite()'.

A progress bar is shown during the download process. The final data is saved as 'bigg_universal_metabolit_database' in the specified path. If 'delete_intermediate = TRUE', intermediate files are deleted after the download completes.

Value

None. The function saves the downloaded data to the specified directory.

Examples

## Not run: 
# Download BiGG universal metabolite data to the current directory
download_bigg_universal_metabolite()

# Download data to a custom path with 2 seconds of sleep between downloads
download_bigg_universal_metabolite(path = "data", sleep = 2)

# Keep intermediate files
download_bigg_universal_metabolite(delete_intermediate = FALSE)

## End(Not run)

tidymass/massdatabase documentation built on Oct. 18, 2024, 3:56 p.m.