set_synapse_credentials: Connect to 'Synapse' API

In genieBPC: Project GENIE BioPharma Collaborative Data Processing Pipeline

Connect to 'Synapse' API

Description

This function sets 'Synapse' credentials for the user's current session.

Usage

set_synapse_credentials(pat = NULL)

Arguments

pat	'Synapse' Personal Access Token. If NULL, package will search environmental variables for 'SYNAPSE_PAT'.

Details

To access data, users must have a valid 'Synapse' account with permission to access the data set and they must have accepted any necessary 'Terms of Use'. Users must authenticate themselves in their current R session. (See README 'Data Access and Authentication' at https://genie-bpc.github.io/genieBPC/ for details). To set your 'Synapse' Personal Access Token (PAT) during each session, call: 'set_synapse_credentials(pat = "your_pat")'.

If your credentials are stored as an environmental variable, you do not need to call 'set_synapse_credentials()' explicitly each session. To store authentication information in your environmental variables, add the following to your .Renviron file, then restart your R session (tip: you can use 'usethis::edit_r_environ()' to easily open/edit this file):

• 'SYNAPSE_PAT = <your-pat>'

Alternatively, you can pass your PAT to each individual data pull function if preferred, although it is recommended that you manage your PATs outside of your scripts for security purposes.

Value

A success message if you credentials are valid for 'Synapse' platform; otherwise an error

Author(s)

Karissa Whiting

Examples

## Not run: 
set_synapse_credentials(
  pat = "your-personal-access-token"
)

## End(Not run)

genieBPC documentation built on April 21, 2026, 1:06 a.m.