pull_data_synapse() function accesses the specified
version of the clinical and genomic GENIE BPC data from Synapse
and reads it into the R environment.
This vignette will walk a user through the
Access to the GENIE BPC data release folders on ‘Synapse’ is required in order to use this function. To obtain access:
For public data releases:
Select Request Access, review the terms of data use and select Accept
Note that permissions for Synapse and permissions for each data release are distinct. Both permissions must be accepted to successfully access the data.
For consortium data releases (restricted to GENIE consortium members & BPC pharmaceutical partners):
Register for a ‘Synapse’ account
Use this link to access the GENIE BPC team list and request to join the team. Please include your full name and affiliation in the message before sending out the request.
Once the request is accepted, you may access the data in the GENIE Biopharma Collaborative projects.
Note: Please allow up to a week to review and grant access.
set_synapse_credentials(username = "your_username", password = "your_password")
If your credentials are stored as environmental variables, 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
SYNAPSE_USERNAME = <your-username>
SYNAPSE_PASSWORD = <your-password>
Alternatively, you can pass your username and password to each individual data pull function if preferred, although it is recommended that you manage your passwords outside of your scripts for security purposes.
Let’s start by reviewing the
||Vector or list specifying the cohort(s) of interest. Must be one of 'NSCLC' (Non-Small Cell Lung Cancer), 'CRC' (Colorectal Cancer), or 'BrCa' (Breast Cancer)|
||Vector specifying the version of the data. Must be one of the following: 'v1.1-consortium', 'v1.2-consortium', 'v2.1-consortium', 'v2.0-public'. When entering multiple cohorts, the order of the version numbers corresponds to the order that the cohorts are specified; the cohort and version number must be in the same order in order to pull the correct data.|
||If `NULL` (default), data will be returned as a list of dataframes with requested data as list items. Otherwise, specify a folder path to have data automatically downloaded there. When a path is specified, data are not read into the R environment.|
Pull version 2.0-public of the NSCLC data from Synapse and store in the local environment.
= pull_data_synapse("NSCLC", version = "v2.0-public")nsclc_2_0
nsclc_data object is a list of elements,
such that each element represents a dataset:
Pull version 2.1-consortium of the NSCLC data and version 1.1-consortium of the CRC data.
pull_data_synapse(c("NSCLC", "CRC"), version = c("v2.1-consortium","v1.1-consortium"))
Pull version 1.2-consortium of the NSCLC data and version 1.1-consortium of the CRC data.
pull_data_synapse(c("NSCLC", "CRC"), version = c("v1.2-consortium", "v1.1-consortium"))