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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

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) { # \dontrun{
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
)
} # }