The 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
pull_data_synapse()
function.
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:
Register for a ‘Synapse’ account. Be sure to create a username and password. Note: do NOT connect via your Google account.
Accept the Synapse account terms of use.
Navigate to GENIE Biopharma Collaborative Public page.
In the Files folder, navigate to Data Releases and click on the cancer cohort and data release version of choice.
Select Request Access, review the terms of data use, and select Accept.
For consortium data releases (restricted to GENIE consortium members & BPC pharmaceutical partners):
Register for a ‘Synapse’ account. Be sure to create a username and password. Note: do NOT connect via your Google account.
Accept the Synapse account terms of use.
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. (Note: Please allow up to a week to review and grant access.)
Once the request is accepted, you may access the data in the GENIE Biopharma Collaborative projects.
In the Files folder, navigate to Data Releases and click on the cancer cohort and data release version of choice.
Select Request Access, review the terms of data use, and select Accept.
Note: permissions for Synapse and permissions for each data release are distinct. Both permissions must be accepted to successfully access the data.
Authenticate yourself
Whether you are using public or consortium data, you will need to authenticate yourself at the beginning of each R session in which you use {genieBPC} to pull data. To set your Synapse credentials during each session, call:
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
file):
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 pull_data_synapse()
arguments.
Argument | Description |
---|---|
|
Vector or list specifying the cohort(s) of interest. Must be one of 'NSCLC' (Non-Small Cell Lung Cancer), 'CRC' (Colorectal Cancer), 'BrCa' (Breast Cancer), 'BLADDER' (Bladder Cancer), 'PANC' (Pancreatic Cancer), or 'Prostate' (Prostate 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. |
|
Synapse username |
|
Synapse password |
Pull version 2.0-public of the NSCLC data from Synapse and store in the local environment.
The resulting nsclc_2_0
object is a list of elements,
such that each element represents a dataset:
Pull version 2.2-consortium of the NSCLC data and version 1.3-consortium of the CRC data.
Please note that pulling genomic GENIE data from Synapse using
pull_data_synapse()
and pulling GENIE data from cBioPortal
may result in small differences in the data due to systematic
differences in the processing pipelines employed by Synapse and
cBioPortal. These differences may include:
Data formatting - Some data sets (e.g. CNA files) may appear in wide format in Synapse data versus long format in cBioPortal data, or column attributes and names may appear sightly different (e.g. fusions files).
Default filtering - By default, cBioPortal filters out Silent, Intron, IGR, 3’UTR, 5’UTR, 3’Flank and 5’Flank, except for the promoter mutations of the TERT gene. See cBioPortal documentation for more details. These mutations are retained in Synapse processing pipelines.
Hugo Symbols - Some genes have more than one accepted Hugo Symbol
and may be referred to differently between data sources
(e.g. NSD3
is an alias for WHSC1L1
). Some
tools exist to help you resolve gene aliases across genomic data
sources. See gnomeR::recode_alias()
,
cbioportal::get_alias()
and vignettes from the {gnomeR} and {cbioportalR} for
more information on how to use these functions and work with gene
aliases.