Get tables with custom fields

A convenience function to quickly fetch table of Gene IDs, Protein IDs, Gene Symbols, Annotations and many more columns from database of your choice such as PlasmoDB, ToxoDB, PiroplasmaDB among other VEuPathDB pathogen databases.

Usage

getTable(
  org,
  db = "toxodb",
  customFields = NULL,
  api_key = Sys.getenv("VEUPATHDB_API_KEY")
)

Arguments

org

Full name of organism of interest as specified in VEuPathDB. To find the exact name of the organism, use listVeupathdb function.

db

Character Name of the database in which the organism is present. These can be one of the following: "toxodb","plasmodb","hostdb","amoebadb","cryptodb","fungidb","giardiadb","microsporidiadb","piroplasmadb","trichdb","tritrypdb".

customFields

A vector of custom fields desired to be fetched. "primary_key" is mandatory field. Use getTableAttributes() to browse the attributes available for the selected database and record type. If NULL, a default set of attributes is returned.

api_key

VEuPathDB API key.

Value

A data frame, containing "Gene ID", "Product Description", "Gene Strand", "Gene Name or Symbol", "Previous ID(s)", "Entrez Gene ID", "UniProt ID(s)", "Protein Length", "TM Domains" and "SignalP Peptide" for all the genes present in the organism of interest.

Details

With release 71 of VEuPathDB, only users with subscription and API key can access the database programmatically. Use usethis::edit_r_environ(scope = "user") to add VEuPathDB API using VEUPATHDB_API_KEY variable.

See also

getTableAttributes() for browsing the attributes available for a given record type.

Examples

if (FALSE) { # \dontrun{

df <- getTable(org="Plasmodium falciparum 3D7", 
db="plasmodb",api_key = Sys.getenv("VEUPATHDB_API_KEY"))

df <- getTable(org="Plasmodium falciparum 3D7", 
db="plasmodb", api_key = Sys.getenv("VEUPATHDB_API_KEY"), 
customFields = c("primary_key","protein_sequence"))
} # }