Retrieve accession numbers and titles for a genbank search

Retrieve accession numbers and titles for searches in genbank. This function is useful for exploring the gene-, population-, and species-level sampling in genbank.

Usage

acc.retrieve(
  organism,
  acc.num = FALSE,
  gene = NULL,
  speciesLevel = FALSE,
  npar = 2,
  nSearchesBatch = 499
)

Arguments

organism

The name of a single taxon (character).

acc.num

Logical indicating whether the organism is actually a vector or accession numbers.

gene

The name of a single gene region (character; optional).

speciesLevel

Whether the result should be a species-level dataset (logical).

npar

Number of parallel searches (the default is probably the best option).

nSearchesBatch

Number of searches per batch

Value

This function returns an object of class data.frame that includes the following columns. First, Species with the species name listed in GenBank. Second, Ti including the title of the accession in GenBank. Third, Acc listing the accession number. Fourth, gene including the name of the target gene.

Examples

if (FALSE) {
acc.retrieve(organism="Vulpes", gene = 'cytb', species=TRUE)
}