Establish connection to biomaRt database — load

This function establishes a connection to a biomart database.

load_mart(species, ensembl.path = "www.ensembl.org", mart, verbose = FALSE)

Arguments

species: The species of the protein identifiers in the term used by biomaRt (e.g. "hsapiens_gene_ensembl", "mmusculus_gene_ensembl", "drerio_gene_ensembl", etc.)
ensembl.path: Ensembl host to connect to. Default: www.ensembl.org
mart: The type of mart (e.g. "ENSEMBL_MART_ENSEMBL", etc.)
verbose: print a summary of the ensembl connection.

Value

Connection for performing biomart queries.

Author

Peter Blattmann

Examples

{
 data_table <- data.frame(Protein = c("Q01581", "P49327", "2/P63261/P60709"),
                          Abundance = c(100, 3390, 43423))
 mart <- convert_protein_ids(data_table)
 }
#> Warning: Ensembl will soon enforce the use of https.
#> Ensure the 'host' argument includes "https://"