| Title: | Signatures for single-cell data analysis |
|---|---|
| Description: | A database of useful signatures for single-cell data analysis. Query the existing signatures or use it to organize your own gene sets in a hierarchical structure. |
| Authors: | Massimo Andreatta [aut, cre] (ORCID: <https://orcid.org/0000-0002-8036-2647>), Paul Gueguen [aut] (ORCID: <https://orcid.org/0000-0003-2930-6073>), Santiago Carmona [aut] (ORCID: <https://orcid.org/0000-0002-2495-0671>) |
| Maintainer: | Massimo Andreatta <[email protected]> |
| License: | GPL-3 |
| Version: | 0.3.0 |
| Built: | 2026-05-14 06:57:22 UTC |
| Source: | https://github.com/carmonalab/SignatuR |
Add a new internal node to the DB. This generates a local, updated copy of the database.
AddNode(db, parent_node, name = "New_signature", reference = NA)AddNode(db, parent_node, name = "New_signature", reference = NA)
db |
The database object to be updated |
parent_node |
The parent node where the new node should be added |
name |
Name for the new node |
reference |
Optional text to describe the node |
An update database containing the new node
data(SignatuR) SignatuR <- AddNode(SignatuR, parent_node=SignatuR$Hs, name="New_category")data(SignatuR) SignatuR <- AddNode(SignatuR, parent_node=SignatuR$Hs, name="New_category")
Add a new signature to the DB. This generates a local, updated copy of the database.
AddSignature( db, node, name = "New_signature", signature = NULL, reference = NA, overwrite = FALSE )AddSignature( db, node, name = "New_signature", signature = NULL, reference = NA, overwrite = FALSE )
db |
The database object to be updated |
node |
A database node where the new signature should be added |
name |
Signature name |
signature |
Gene signature, as a vector of genes |
reference |
A text describing source of the signature or other comments |
overwrite |
Whether to replace an already existing signature with the same name |
An update database containing the new signature
data(SignatuR) SignatuR <- AddSignature(SignatuR, node=SignatuR$Mm$Cell_types, name="T_cell", reference="A simple T cell signature", signature=c("Cd2","Cd3d","Cd3e"))data(SignatuR) SignatuR <- AddSignature(SignatuR, node=SignatuR$Mm$Cell_types, name="T_cell", reference="A simple T cell signature", signature=c("Cd2","Cd3d","Cd3e"))
Return one or more signatures from a specified database node. If an intermediate node is specified, all signatures below that node are returned as a list of signatures.
GetSignature(node)GetSignature(node)
node |
A database node, either internal or leaf |
A single signature or list of signatures
data(SignatuR) # Single signature GetSignature(SignatuR$Mm$Programs$HeatShock) # Multiple signature from intermediate node s <- GetSignature(SignatuR$Mm$Programs) lapply(s, head)data(SignatuR) # Single signature GetSignature(SignatuR$Mm$Programs$HeatShock) # Multiple signature from intermediate node s <- GetSignature(SignatuR$Mm$Programs) lapply(s, head)
Load a file storing a SignatuR object. See also the function SaveSignatuR for saving existing DB.
LoadSignatuR(file = "mySignatuR.csv")LoadSignatuR(file = "mySignatuR.csv")
file |
Source file (.csv, .rds or .rda) |
A SignatuR object
data(SignatuR) # Save DB SaveSignatuR(SignatuR, file="mySignatuR.csv") # Load it back mySignatuR <- LoadSignatuR("mySignatuR.csv")data(SignatuR) # Save DB SaveSignatuR(SignatuR, file="mySignatuR.csv") # Load it back mySignatuR <- LoadSignatuR("mySignatuR.csv")
Remove a given signature or node from the database
RemoveSignature(node)RemoveSignature(node)
node |
A database node to be removed |
Nothing. The DB is modified in place.
data(SignatuR) RemoveSignature(SignatuR$Hs$Compartments$TCR)data(SignatuR) RemoveSignature(SignatuR$Hs$Compartments$TCR)
Store a modified copy of your SignatuR DB, in different formats. Saving to .csv allows editing of signatures in a text or spreadsheet program
SaveSignatuR(db, file = "mySignatuR.csv")SaveSignatuR(db, file = "mySignatuR.csv")
db |
The database object to be saved |
file |
Destination file (.csv, .rds or .rda) |
data(SignatuR) # Save DB SaveSignatuR(SignatuR, file="mySignatuR.csv") # Load it back mySignatuR <- LoadSignatuR("mySignatuR.csv")data(SignatuR) # Save DB SaveSignatuR(SignatuR, file="mySignatuR.csv") # Load it back mySignatuR <- LoadSignatuR("mySignatuR.csv")
The DB is structured in a tree format, using the data.tree data type. See the examples below to browse and access this data type.
print(SignatuR)
SignatuRSignatuR
A data.tree object with signatures organized by species and category. Gene lists are stored in the "Signature" attribute,
comments and references for the signature are stored in the "Reference" attribute.
SignatuR
print(SignatuR, "Reference","Signature")
library(DiagrammeR) plot(SignatuR)
GetSignature(SignatuR$Mm$Programs$HeatShock)
GetSignature(SignatuR$Mm$Programs)
SignatuR <- AddSignature(SignatuR, node=SignatuR$Mm$Cell_types,name="T_cell", reference="A simple T cell signature", signature=c("Cd2","Cd3d","Cd3e")
SignatuR <- AddNode(SignatuR, parent_node=SignatuR$Hs, name="New_category")
SaveSignatuR(SignatuR, file="mySignatuR.csv")
mySignatuR <- LoadSignatuR("mySignatuR.csv")
usethis::use_data(SignatuR, overwrite = TRUE)