Get pre-configured tables — getPreconfiguredTable • plasmoRUtils

A convenience function to quickly fetch preconfigured table of Signal Peptide ranges, Pathways, Pubmed entries related to genes, Annotations and etc from database of your choice such as PlasmoDB, ToxoDB, PiroplasmaDB among other VEuPathDB pathogen databases.

Usage

getPreconfiguredTable(
  org = NULL,
  db = "plasmodb",
  customField = "Y2hInteractions",
  listtables = FALSE,
  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".
customField: Preconfigured table that you wish the fetch. Pass only one value at a time from the following: "GeneModelDump", "GeneTranscripts", "Alias", "GeneLinkouts", "GeneLocation", "PubMed", "OrthologsLite", "LowComplexity", "PdbSimilarities", "3dPreds", "AlphaFoldLinkouts", "ProteinProperties", "InterPro", "SignalP", "TMHMM", "ECNumbers", "ECNumbersInferred", "protein_length", "chromosome", "location_text", "sequence_id", "gene_ortholog_number", "gene_orthomcl_name", "gene_paralog_number", "MetabolicPathwaysMPMP", "MetabolicPathways", "CompoundsMetabolicPathways", "Y2hInteractions", "MassSpecDownload", "MassSpecMod", "Epitopes" etc. You can view list of 58 preconfigured tables across VEuPathDB databases using getPreconfiguredTable(listtables = TRUE)
listtables: To get list of preconfigured tables that can be supplied as an argument to customField.
api_key: Character. VEuPathDB API key used for authentication. By default, the value is obtained from the VEUPATHDB_API_KEY environment variable.

Value

A data frame.

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.

Examples

if (FALSE) { # \dontrun{
getPreconfiguredTable(listtables = TRUE)
df <- getPreconfiguredTable(org = "Plasmodium falciparum 3D7",
     db = "plasmodb",customField = "Y2hInteractions")
} # }