README

Callen & Vanessa April 14, 2021

SigRepoR

Last update

April 14, 2021

Contacts

Callen Bragdon - cjoseph@bu.edu

Vanessa Mengze Li - vmli@bu.edu

SigRepo Components

Back-end: MariaDB
R functions to interact with DB: This package SigRepoR. See Installation below.
R6 objects: OmicSignature and OmicSignatureCollection designed to store signatures. See Installation below. Click here for the vignette
User-control API
Front-end: R-Shiny interface

See our development Shiny app server (BU VPN required)

Installation

devtools::install_github(repo = "montilab/OmicSignature")

devtools::install_github(repo = "montilab/SigRepoR", auth_token = "...")

Manual of uploading signatures into Database

Configuration and Setup

Before proceeding with any interactions, it's important that you first configure your session to point to which database to upload to, along with where to write files to in your file system.

configureSigRepo(
  signatureDirectory="/opt/shiny-server/challenge_project/miscellanea/signatures/",
  databaseServer="sigrepo.bu.edu",
  databasePort="4253",
  applicationPort="",
  signatureServer="sigrepo.bu.edu"
)

Now, for downstream queries, you'll be able to establish connections in the future without needing to specify which server to query repeatedly.

The final step in your setup will be to establish your connection handle, described below:

myHandle <- newConnHandle("cjoseph", usePassword="NO")

You will be prompted to (safely) enter your password in another dialogue window in order to establish a connection to your database.

However, if you don't need any particular permissions, and just want to "read only", you can create a handle with the "guest" account, which only has read privileges and are the default parameters for establishing this handle, shown below.

myHandle <- newConnHandle()

For certain R querying functions in this package, the guest account is used by default, and the handle disconnects when accomplishing the query by default.

Assuming you already have your OmicSignature object created, let's work with uploading.

Requesting Upload Privileges

If you don't have "write" access, after configuration, you can use requestUser(), which will add your table to the "user_requests" table in the database for review by an administrator, who will use userApproval to either grant or reject your request

# you can choose not to put
# parameters in, and use the console
# readline capability to fill them in as you go.
requestUser(
  newUserName="requestedName", 
  newUserEmail="example@test.edu"
)
# you'll still be prompted for a password you would want to use

Uploading OmicSignature Object

To upload your object completely to your back-end

addSignatureWrapper(
    yourObjectOrFileOfObject,
    thisHandle=yourConnectionHandle,
    # uploadPath=sys.getenv("signatureDirectory"), # default to configuration settings
    user="your SigRepo Username"
)

executing the above:

writes your object and differential expression files to disk
checks the phenotype of the signature object. if it doesn't exist already in the phenotypes table, that new phenotype will get added.
inserts signature metadata into signatures table in the database(addSignature)
inserts level2 data from that object into the features_signatures table in the database(addLevel2).
inserts signature-keyword pairs into the keyword_signatures table in the database(addSignatureKeywords).

Uploading OmicSignatureCollection Objects

OmicSignatureCollection Objects are simply a group of Omic Signature objects. You can upload such objects like this:

addSignatureCollection(
    OmicSignatureCollectionObj, 
    connHandle,
  uploadPath=sys.getenv("signatureDirectory"), 
  thisUser="your SigRepo User Name"
)

This function:

"unpacks" the OmicSignatureCollection by getting the "OmicSigList" property
runs an lapply of the function "addSignatureWrapper" on this list
inserts signature-to-collection pairs into the signature-to-collection table in the database(addCollectionSignatures)

If the collection you're uploading doesn't exist as an entry in the collections table of the database, the addCollectionSignatures function will add that collection as a new entry to the collections table before uploading the pairs.