View source: R/acc.table.retrieve.R
acc.table.retrieve | R Documentation |
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.
acc.table.retrieve(
clades = NULL,
species = NULL,
genes = NULL,
speciesLevel = NULL,
npar = 2,
nSearchesBatch = 499
)
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 |
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.
## Not run:
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
)
## End(Not run)
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