Add organisms to database
Arguments
- conn_handler
An R object obtained from SigRepo::newConnhandler() (required)
- organism_tbl
A Data Frame; Must contain the following column names: organism, biomart_db, biomart_dataset, biomart_description, biomart_version, biomart_updated_date, prot_organism_code, prot_organism_taxid, prot_updated_date (required)
- verbose
Logical; whether to print diagnostic messages. Defaults to 'TRUE'
Examples
if (FALSE) { # \dontrun{
# Create organisms table
organism_tbl <- base::data.frame(
organism = "Homo sapiens",
biomart_db = "genes",
biomart_dataset = "hsapiens_gene_ensembl",
biomart_description = "Human genes (GRCh38.p14)",
biomart_version = 114,
biomart_updated_date = base::as.Date(base::Sys.Date(), format = "%Y-%m-%d"),
prot_organism_code = "Human",
prot_organism_taxid = 9606,
prot_updated_date = base::as.Date(base::Sys.Date(), format = "%Y-%m-%d")
)
# Create a connection handler
conn_handler <- SigRepo::newConnHandler(
dbname = "sigrepo",
host = "sigrepo.org",
port = 3306,
user = "your_username",
password = "your_password"
)
# Add organisms to database
SigRepo::addOrganism(
conn_handler = conn_handler,
organism_tbl = organism_tbl,
verbose = TRUE
)
} # }