SigRepo: An R package for storing and processing omic signatures

The SigRepo package provides a comprehensive set of functions for easy storage and management of biological signatures and their components. SigRepo (the client) works alongside SigRepo_Server, its server counterpart. While SigRepo enables you to store, search, and retrieve signatures and signature collections, these operations rely on 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 utilize the functionalities offered by the SigRepo package — signatures and signature collections must be represented as specific R6 objects. You can create these objects using our proprietary 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 devtools package

# 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 navigate to our sigrepo.org portal to create your account. On the login page, click "Register here!" and fill out the registration form to create an account. You will receive an email when your account has been activated. Due to SQL constraints, having multiple users on the same testing account, like running the tutorial in the readme, will fail to connect. Each user using their own account is ideal.

Visibility

The SigRepo Project is a project that holds various sensitive signatures. Because of this, visibility of certain signatures is taken into account. What this means is that in order to retrieve certain signatures with the visibility of private(visibility = 0), standard accounts will not be able to access that signature and you will need permission from the signature author to access it. Conversely, a signature with the visibility of public (visibility = 1, this is also the DEFAULT) will be available to everyone with an account. Please note, viewing a signature with searchSignature() is different than using getSignature(), searchSignature() only shows the metadata of the signature and this is shown to everyone. getSignature takes into account the visibilty of the signatures.

Connect to SigRepo Database

SigRepo uses a MySQL database to store, search, and retrieve biological signatures and their components. To access signatures in our database, VISIT OUR WEBSITE to create an account or CONTACT US to be added.

There are three types of user accounts:
- admin has READ and WRITE access to all signatures in the database.
- editor has READ and WRITE access to only their own uploaded signatures in the database.
- viewer has READ-ONLY access to publicly available signatures in the database.

Once you have a valid account, use SigRepo::newConnHandler() to create a handler with your credentials.

# Create a connection handler
conn_handler <- SigRepo::newConnHandler(
  dbname = "sigrepo", 
  host = "sigrepo.org", 
  port = 3306, 
  user = <your_username>, 
  password = <your_password>
)

After you call newConnHandler(), SigRepo stores that handler internally for the current R session.
Because of that, most SigRepo functions can be called in either of these ways:

1. Explicitly pass conn_handler in each call.
2. Omit conn_handler and use the internally stored handler.

# Option 1: explicit connection handler
SigRepo::searchSignature(
  conn_handler = conn_handler,
  signature_name = "example_signature"
)

# Option 2: use stored handler from newConnHandler()
SigRepo::searchSignature(
  signature_name = "example_signature"
)

Guides

• Uploading Signature Tutorial
• Uploading Signature Collection Tutorial