The SigRepo package provides a comprehensive set of functions for storing, managing, and interacting with biological signatures and their components. SigRepo (the client) works in tandem with SigRepo_Server, its server-side counterpart. While SigRepo allows you to store, search, and retrieve signatures and signature collections, all such operations require access to a running SigRepo_Server instance.
Interested in setting up your own SigRepo_Server? Check out the installation instructions here.
To upload and download signatures—and to fully leverage the functionality of the SigRepo package—signatures and signature collections must be represented as specific R6 objects. These objects are created using our companion package, OmicSignature.
Click on each link below for more information:
- Overview of the object structure
- Create an OmicSignature (OmS)
- Create an OmicSignatureCollection (OmSC)
Below, we walk you through few essential steps to install the SigRepo package, and to store, retrieve, and interact with a list of signatures stored in an already deployed SigRepo server.
Installation
- Using
devtoolspackage
# Load devtools package
library(devtools)
# Install SigRepo
devtools::install_github(repo = 'montilab/SigRepo')
# Install OmicSignature
devtools::install_github(repo = 'montilab/OmicSignature')
# Load tidyverse package
library(tidyverse)
# Load SigRepo package
library(SigRepo)
# Load OmicSignature package
library(OmicSignature)Before you begin
Please visit sigrepo.org to create an account. On the login page, click “Register here!” and complete the registration form. You will receive an email once your account has been activated.
Due to SQL constraints, multiple users sharing the same testing account (for example, when following the README tutorial) may encounter connection failures. We strongly recommend that each user create and use their own account.
Visibility
SigRepo hosts a collection of potentially sensitive biological signatures, so access control is enforced through visibility settings.
Private signatures (visibility = 0) are accessible only to the signature author and users who have been granted explicit permission.
Public signatures (visibility = 1, the default) are accessible to all registered users.
Note that searchSignature() and getSignature() behave differently:
searchSignature() returns metadata only and is visible to all users, regardless of signature visibility.
getSignature() retrieves the full signature and enforces visibility restrictions.
Connect to the SigRepo Database
SigRepo uses a MySQL database to efficiently store, search, and retrieve biological signatures and their associated components. To access the database, you must create an account via our website or contact us to be added.
There are three user account types:
admin: Read and write access to all signatures.
editor: Read and write access only to signatures they have uploaded.
viewer: Read-only access to publicly available signatures.
Once you have a valid account, you can connect to the SigRepo database using the SigRepo::newConnHandler() function, which creates a connection handler containing your credentials.