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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, db = "plasmodb", customField = "Y2hInteractions")

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.

Value

A data frame.

Examples

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