List genomes and metadata in VEuPathDB

A convenience function to quickly fetch table of genomes and their associated metadata from VEupathDB.

Usage

listVeupathdb(
  customFields = NULL,
  api_key = Sys.getenv("VEUPATHDB_API_KEY"),
  timeout = 60,
  max_tries = 3
)

Arguments

customFields

A vector of custom fields desired to be fetched. "primary_key" is mandatory field. Other fields can be supplied and can be chosen from (but are not limited to): "annotation_source", "annotation_version", "arraygenecount", "chipchipgenecount", "chromosomeCount", "codinggenecount", "communitycount", "contigCount", "ecnumbercount", "estcount", "genecount", "genecount_number", "genome_source", "genome_version", "gocount", "is_in_apollo", "is_reference_strain", "megabps", "ncbi_tax_id", "ncbi_taxon_url", "organism", "organism_full", "orthologcount", "othergenecount", "popsetcount", "project_id", "proteomicscount", "pseudogenecount", "rnaseqcount", "rtpcrcount", "snpcount", "species", "species_ncbi_tax_id", "species_ncbi_taxon_url", "supercontigCount", "tfbscount", "URLcdsFasta", "URLGenomeFasta", "URLgff", "URLproteinFasta", "URLtranscriptFasta". For more fields, refer to the VEuPathDB Documentation

api_key

Character. VEuPathDB API key used for authentication. By default, the value is obtained from the VEUPATHDB_API_KEY environment variable.

timeout

Timeout time in seconds. Defaults to 60.

max_tries

Maximum number of request attempts. Defaults to 3.

Value

A data frame containing information about genomes present in VEuPathDB and their attributes.

Examples

if (FALSE) { # \dontrun{
df <- listVeupathdb()
df <- listVeupathdb(customFields=c("species", "project_id"))
} # }