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.