
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
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
)
}