Main retrieval function for coding sequences (CDS) of an organism of interest. By specifying the scientific name of an organism of interest the corresponding fasta-file storing the CDS information for the organism of interest can be downloaded and stored locally. CDS files can be retrieved from several databases.
Usage
getCDS(
db = "refseq",
organism,
reference = FALSE,
release = NULL,
gunzip = FALSE,
path = file.path("_ncbi_downloads", "CDS")
)
Arguments
- db
a character string specifying the database from which the genome shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
- organism
there are three options to characterize an organism:
by
scientific name
: e.g.organism = "Homo sapiens"
by
database specific accession identifier
: e.g.organism = "GCF_000001405.37"
(= NCBI RefSeq identifier forHomo sapiens
)by
taxonomic identifier from NCBI Taxonomy
: e.g.organism = "9606"
(= taxid ofHomo sapiens
)
- reference
a logical value indicating whether or not a genome shall be downloaded if it isn't marked in the database as either a reference genome or a representative genome.
- release
the database release version of ENSEMBL (
db = "ensembl"
). Default isrelease = NULL
meaning that the most recent database version is used.- gunzip
a logical value indicating whether or not files should be unzipped.
- path
a character string specifying the location (a folder) in which the corresponding CDS file shall be stored. Default is
path
=file.path("_ncbi_downloads","CDS")
.
Examples
if (FALSE) {
# download the genome of Arabidopsis thaliana from refseq
# and store the corresponding genome CDS file in '_ncbi_downloads/CDS'
file_path <- getCDS( db = "refseq",
organism = "Arabidopsis thaliana",
path = file.path("_ncbi_downloads","CDS"))
Ath_CDS <- read_cds(file_path, format = "fasta")
}