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Signature Collection Tutorial

Source: vignettes/collection-tutorials.Rmd
collection-tutorials.Rmd

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 packages 

# Load tidyverse package
library(tidyverse)

# Load SigRepo package
library(SigRepo)

# Load OmicSignature package
library(OmicSignature)

Create a handler to connect to SigRepo Database 

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

Load signatures

Here, we provided 4 signature objects that came with the package for demonstrations:

  1. omic_signature_1 (Myc_reduce_mice_liver_24m_v1)
  2. omic_signature_2 (Myc_reduce_mice_liver_24m_v2)
  3. omic_signature_3 (Myc_reduce_mice_liver_24m_v3)
  4. omic_signature_4 (Myc_reduce_mice_liver_24m_v4)
# Read in the signature objects
omic_signature_1 <- base::readRDS(base::file.path(base::system.file("inst/extdata", package = "SigRepo"), "omic_signature_1.rds"))
omic_signature_2 <- base::readRDS(base::file.path(base::system.file("inst/extdata", package = "SigRepo"), "omic_signature_2.rds"))
omic_signature_3 <- base::readRDS(base::file.path(base::system.file("inst/extdata", package = "SigRepo"), "omic_signature_3.rds"))
omic_signature_4 <- base::readRDS(base::file.path(base::system.file("inst/extdata", package = "SigRepo"), "omic_signature_4.rds"))

Create an omic collection

Here, we will create a collection with two signatures, omic_signature_1 and omic_signature_1, provided above. See ?OmicSignatureCollection() from OmicSignature package for more details on how to create an omic collection object.

# Create a metadata object for the collection
metadata <- base::list(
  "collection_name" = "my_collection",
  "description" = "An example of signature collection"
)

# Create an omic collection using OmicSignatureCollection() from OmicSignature package
omic_collection <- OmicSignature::OmicSignatureCollection$new(
  OmicSigList = base::list(omic_signature_1, omic_signature_2),
  metadata = metadata
)
#>   [Success] OmicSignature Collection my_collection created.

Upload a collection to the database

The SigRepo::addCollection() function allows users to upload a collection to the database.

IMPORTANT NOTE:

SigRepo::addCollection(
  conn_handler = conn_handler,        # A handler contains user credentials to establish connection to a remote database
  omic_collection = omic_collection,  # An R6 object obtained from OmicSignature::OmicSignatureCollection()
  visibility = FALSE,                 # Whether to make the collection public or private. Default is FALSE.
  return_collection_id = FALSE,       # Whether to return the uploaded collection id. Default is FALSE.
  verbose = TRUE                      # Whether to print diagnostic messages. Default is TRUE.
)
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v2 created.
#>   [Success] OmicSignature Collection my_collection created.
#> Uploading each signature in the collection to the database...
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v2 created.
#> Uploading collection metadata to the database...
#> Adding user to collection access table in the database...
#> Adding signature to the collection access table of the database...
#> Finished uploading.
#> ID of the uploaded collection: 168

Search for a collection in the database

The SigRepo::searchCollection() function allows users to retrieve all collections that are available in the database.

Example 1: Search for all collections 

# Get all collections
collection_tbl_1 <- SigRepo::searchCollection(conn_handler = conn_handler)

# WARNINGS: THE COLLECTION TABLE CAN BE LARGE, SO ONLY THE FIRST SIX OBSERVATIONS ARE SHOWN.
if(base::nrow(collection_tbl_1) > 0){
  knitr::kable(
    utils::head(collection_tbl_1), 
    row.names = FALSE
  )
}
collection_id collection_name description user_name date_created visibility collection_hashkey signature_id signature_collection_hashkey signature_name
61 Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024 aging‐associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results H_Nikoueian 2025-10-03 15:09:35 0 47b45086ae30d329d17ad93db68479de 213 4abdc3cd86a6f59eeb33ac7bf55252e2 Aging_Hs_HNSC_RNASeq_TCGA_ACC_MontiLab2025
61 Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024 aging‐associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results H_Nikoueian 2025-10-03 15:09:35 0 47b45086ae30d329d17ad93db68479de 214 8b4077aa6a4434add27043542cad2e8a Aging_Hs_HNSC_RNASeq_TCGA_BLCA_MontiLab2025
61 Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024 aging‐associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results H_Nikoueian 2025-10-03 15:09:35 0 47b45086ae30d329d17ad93db68479de 215 43d0193b623ae62359f03ad342298498 Aging_Hs_HNSC_RNASeq_TCGA_BRCA_MontiLab2025
61 Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024 aging‐associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results H_Nikoueian 2025-10-03 15:09:35 0 47b45086ae30d329d17ad93db68479de 216 f984e7003314d15197a30d239df47b01 Aging_Hs_HNSC_RNASeq_TCGA_CESC_MontiLab2025
61 Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024 aging‐associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results H_Nikoueian 2025-10-03 15:09:35 0 47b45086ae30d329d17ad93db68479de 217 82fae89f903a358b58654d5e2f2d33c8 Aging_Hs_HNSC_RNASeq_TCGA_COAD_MontiLab2025
61 Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024 aging‐associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results H_Nikoueian 2025-10-03 15:09:35 0 47b45086ae30d329d17ad93db68479de 218 6498fece50ede60a446812e25f080c7d Aging_Hs_HNSC_RNASeq_TCGA_ESCA_MontiLab2025

Example 2: Search for a specific collection by its name, e.g., collection_name = "my_collection". 

collection_tbl_2 <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)

if(base::nrow(collection_tbl_2) > 0){
  knitr::kable(
    collection_tbl_2, 
    row.names = FALSE
  )
}
collection_id collection_name description user_name date_created visibility collection_hashkey signature_id signature_collection_hashkey signature_name
168 my_collection An example of signature collection montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 413 c743f5567dcca2a589bd122500a31722 Myc_reduce_mice_liver_24m_v1
168 my_collection An example of signature collection montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 414 68a0652359fc30f530eea8d849f5dd0a Myc_reduce_mice_liver_24m_v2

Retrieve a set of collections in the database

The SigRepo::getCollection() function allows users to retrieve a set of collections that are PUBLICLY available in the database.

IMPORTANT NOTE:

  • Users can ONLY RETRIEVE a list of collections that are publicly available in the database including their own uploaded collections.
  • If a collection is PRIVATE and belongs to other user in the database, users will need to be given an editor permission from its owner to access, retrieve, and edit their collections.

Example 1: Get all collections that are publicly available in the database 

# WARNINGS: THE COLLECTION LIST CAN BE LARGE TO DOWNLOAD (NOT RUN)
collection_list_1 <- SigRepo::getCollection(conn_handler = conn_handler)

Example 2: Get a specific collection that is publicly available or owned by user in the database, e.g., collection_name = "my_collection" 

collection_list_2 <- SigRepo::getCollection(
  conn_handler = conn_handler,
  collection_name = "my_collection"
)
#> now dyn.load("/home/runner/work/_temp/Library/curl/libs/curl.so") ...
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v2 created.
#>   [Success] OmicSignature Collection my_collection created.

Update a collection metadata

The SigRepo::updateCollectionMetadata() function allows users to update the metadata information of a collection in the database.

IMPORTANT NOTE:

  • Users MUST HAVE an editor or admin account to use this function.
  • Furthermore, users can ONLY UPDATE their own uploaded signatures or were given an editor permission from its owner to access, retrieve, and edit their collections.

For example, if you want to change the description of "my_collection" in the database to "This is the updated description." You can use the SigRepo::updateCollectionMetadata() function as follows:

# Let's search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)

# If the collection exists, update it with the new description
if(base::nrow(collection_tbl) > 0){
  SigRepo::updateCollectionMetadata(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id,
    description =  "This is the updated description." 
  )
}
#> collection_id = '168' has been updated.

Now, let’s search for "my_collection" in the database and see if its description has been updated.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)

# If the collection exists, display the table
if(base::nrow(collection_tbl) > 0){
  knitr::kable(
    collection_tbl,
    row.names = FALSE
  )
}
collection_id collection_name description user_name date_created visibility collection_hashkey signature_id signature_collection_hashkey signature_name
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 413 c743f5567dcca2a589bd122500a31722 Myc_reduce_mice_liver_24m_v1
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 414 68a0652359fc30f530eea8d849f5dd0a Myc_reduce_mice_liver_24m_v2

Add signatures to an existing collection in the database

The SigRepo::addSignatureToCollection() function allows users to add a set of signatures to an existing collection in the database.

IMPORTANT NOTE:

  • Users MUST HAVEan editor or admin account to use this function.
  • Furthermore, users can ONLY UPDATE their own uploaded signatures or were given an editor permission from its owner to access, retrieve, and edit their collections.

For example, if you wish to create two new signatures ("omic_signature_3", "omic_signature_4") and add them to "my_collection"in the database.

# Add omic_signature_3 to the database
signature_id_3 <- SigRepo::addSignature(
  conn_handler = conn_handler, 
  omic_signature = omic_signature_3,
  return_signature_id = TRUE,
  verbose = FALSE
)
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v3 created.

# Add omic_signature_4 to the database
signature_id_4 <- SigRepo::addSignature(
  conn_handler = conn_handler, 
  omic_signature = omic_signature_4,
  return_signature_id = TRUE,
  verbose = FALSE
)
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v4 created.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection",
  verbose = FALSE
)

# If both collection and signatures exist, add its signature ids to collection.
if(base::nrow(collection_tbl) > 0 && base::length(signature_id_3) > 0 && base::length(signature_id_4) > 0){
  SigRepo::addSignatureToCollection(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id,
    signature_id =  c(signature_id_3, signature_id_4)
  )
}

Now, let’s search for "my_collection" in the database and see if the signatures are added to the collection.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)

# If collection exists, display the table
if(base::nrow(collection_tbl) > 0){
  knitr::kable(
    collection_tbl,
    row.names = FALSE
  )
}
collection_id collection_name description user_name date_created visibility collection_hashkey signature_id signature_collection_hashkey signature_name
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 413 c743f5567dcca2a589bd122500a31722 Myc_reduce_mice_liver_24m_v1
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 414 68a0652359fc30f530eea8d849f5dd0a Myc_reduce_mice_liver_24m_v2
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 415 77ca7ffeb6e57f62e453193fe4a5ab4a Myc_reduce_mice_liver_24m_v3
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 416 1a7dec419305de845854da969131d2d2 Myc_reduce_mice_liver_24m_v4

Remove a list of signatures from a collection in the database

The SigRepo::removeSignatureFromCollection() function allows users to remove a list of signatures from a collection in the database.

IMPORTANT NOTE:

  • Users MUST HAVEan editor or admin access to use this function.
  • Furthermore, users can ONLY UPDATEtheir own uploaded signatures or were given an editor permission from its owner to access, retrieve, and edit their collections.

For example, if you wish to remove "Myc_reduce_mice_liver_24m_v1" from "my_collection"in the database

# Lets' check if signature = Myc_reduce_mice_liver_24m_v1 is in my_collection
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection",
  signature_name = "Myc_reduce_mice_liver_24m_v1"
)

# If signature collection combo exists, remove the signature.
if(base::nrow(collection_tbl) > 0){
  SigRepo::removeSignatureFromCollection(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id,
    signature_id = collection_tbl$signature_id
  )
}
#> Removing signature_id = '413' from collection_id = '168' completed.

Now, let’s search for "my_collection" in the database and see if signatures have been removed from the collection.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)

# If collection exists, display the table
if(base::nrow(collection_tbl) > 0){
  knitr::kable(
    collection_tbl,
    row.names = FALSE
  )
}
collection_id collection_name description user_name date_created visibility collection_hashkey signature_id signature_collection_hashkey signature_name
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 414 68a0652359fc30f530eea8d849f5dd0a Myc_reduce_mice_liver_24m_v2
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 415 77ca7ffeb6e57f62e453193fe4a5ab4a Myc_reduce_mice_liver_24m_v3
168 my_collection This is the updated description. montilab 2025-10-27 16:30:32 0 a7213731b133effec506851ef7cb443f 416 1a7dec419305de845854da969131d2d2 Myc_reduce_mice_liver_24m_v4

Delete the whole collection from the database

The SigRepo::deleteCollection() function allows users to delete a collection from the database.

IMPORTANT NOTE:

  • Users MUST HAVE an editor or admin account to use this function.
  • Furthermore, users can ONLY DELETE their own uploaded collections or were given an editor permission from other users in the database to access and delete their collection.
  • A collection can ONLY BE REMOVED OR DELETED one at a time.
# Search for my_collection in the database 
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)

# If the collection exists, remove it from the database
if(base::nrow(collection_tbl) > 0){
  SigRepo::deleteCollection(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id
  )
}
#> Remove collection_id = '168' from 'collection' table of the database.
#> Remove collection_id = '168' from 'collection_access' table of the database.
#> Remove signatures belongs to collection_id = '168' from 'signature_collection_access' table of the database.
#> collection_id = '168' has been removed.

Finally, let’s search for "my_collection" in the database and see if the collection has been removed.

collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.