Search for a list of signatures in the database.
Text fields match on one rule, with nothing for the caller to set: a term that is somebody's whole value matches only that value, and a term that is nobody's whole value matches every value containing it. So `signature_name = "M005"` finds every signature with M005 in its name, while `sample_type = "liver"` returns liver signatures and not those whose sample type merely contains the word. Terms are literal: a dot is a dot, and a `%` is a percent sign.
Numbers and controlled vocabularies (`signature_id`, `PMID`, `year`, `has_difexp`, `type`, `assay_type`) always match exactly.
Usage
searchSignature(
conn_handler = NULL,
signature_id = NULL,
signature_name = NULL,
user_name = NULL,
organism = NULL,
phenotype = NULL,
sample_type = NULL,
platform = NULL,
type = NULL,
assay_type = NULL,
keywords = NULL,
description = NULL,
covariates = NULL,
PMID = NULL,
year = NULL,
has_difexp = NULL,
verbose = TRUE
)Arguments
- conn_handler
An R object obtained from SigRepo::newConnhandler() (required)
- signature_id
Database ID of the signatures to be looked up by.
- signature_name
Name of the signatures to be looked up by.
- user_name
The name of the user to be looked up by. The OmicSignature metadata calls this field "author".
- organism
The organism to be looked up by.
- phenotype
The phenotype to be looked up by.
- sample_type
The sample type to be looked up by.
- platform
The platform name to be looked up by.
- type
One or more of `SigRepo::signature_types`.
- assay_type
One or more of `SigRepo::assay_tbl$assay_type`.
- keywords
Keyword text to be looked up by.
- description
Description text to be looked up by.
- covariates
Covariate text to be looked up by.
- PMID
The PubMed ID to be looked up by.
- year
The publication year to be looked up by.
- has_difexp
Whether the signature has a difexp table; TRUE or FALSE.
- verbose
Logical; whether or not to print the diagnostic messages. Defaults to 'TRUE'.
Examples
if (FALSE) { # \dontrun{
# Create a connection handler
conn_handler <- SigRepo::newConnHandler(
dbname = "sigrepo",
host = "sigrepo.org",
port = 3306,
user = "your_username",
password = "your_password"
)
# Search for a list of signatures in the database
SigRepo::searchSignature(
conn_handler = conn_handler,
signature_id = "test_signature",
user_name = "John_Doe"
)
} # }