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Retrieve accession numbers and titles for a given combination of species and genes in genbank

Source: R/acc.table.retrieve.R
acc.table.retrieve.Rd

Retrieve accession numbers and titles for complex searches conducted in genbank. Note that this function depends on acc.retrieve as it actually uses expand.grid to find all the relevant organism/gene combinations in genbank.

Usage

acc.table.retrieve(
  clades = NULL,
  species = NULL,
  genes = NULL,
  speciesLevel = NULL,
  npar = 2,
  nSearchesBatch = 499
)

Arguments

clades

A vector of clade names (character). Note that this can either be the name of a clade (e.g. Apis) or the code in NCBI (e.g. txid7459).

species

A vector of species names (logical). Note that this can either be the name of a clade (e.g. Apis) or the code in NCBI (e.g. txid7459).

genes

A vector of gene names (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

data.frame

Examples

if (FALSE) {
acc.table.retrieve(
 clades  = c('Felis', 'Vulpes', 'Phoca'),
 species = 'Manis_pentadactyla' ,
 genes   = c("A2AB","ADORA3","ADRB2","APOB",
            "APP","ATP7","BCHE","BDNF",
            "BMI1","BRCA1","BRCA2","CNR1",
            "COI","CREM","CYTB","DMP1",
            "EDG1","ENAM","FBN1","GHR",
            "IRBP","ND1","ND2","PLCB4",
            "PNOC","RAG1a","RAG1b","RAG2",
            "TTN","TYR1","VWF"),
 speciesLevel = FALSE
)
}