Retrieve the distribution of genes for given organism in genbank

This function retrieves the gene names for given organism in genbank. This function is useful to explore the genes that are widely sampled for a given taxon in genbank. However, note that the performance of gene.sampling.retrieve is entirely dependant on the quality of submissions to genbank. For instance, if most of the sequences in genbank (nucleotide) don't have information on the sequenced region, this function won't provide reliable estimates of the sampling frequency of each gene in the database. We recommend using this function with caution, and only when there is no additional information on the genes that are widely sampled for the target group(s) of interest.

Usage

gene.sampling.retrieve(
  organism,
  speciesSampling = TRUE,
  npar = 2,
  nSearchesBatch = 499
)

Arguments

organism

A vector of taxonomic groups (character).

speciesSampling

Whether the results should be at the species-level (logical).

npar

Number of simultaneous searches (character; optional). The default 2 is generally fast enough and does not exceed the maximum number of connections to genbank.

nSearchesBatch

Number of searches per batch

Value

This function returns a data.frame that comprises the following columns. First, Gene, including the name of the relevant gene sampled in the target taxonomic groups. Second, Sampled in N species includes the number of species where the gene is sampled among the target taxa. Third, PercentOfSampledSpeciesindicates the percentage of species where the gene is sampled (assuming GeneBank's taxonomic backbone).

Examples

if (FALSE) {
test.spp <- gene.sampling.retrieve(organism = "Puma", speciesSampling = TRUE)
test.pop <- gene.sampling.retrieve(organism = "Puma", speciesSampling = FALSE)
}