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Coding Sequence Retrieval

Source: R/getCDS.R
getCDS.Rd

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 for Homo sapiens)

  • by taxonomic identifier from NCBI Taxonomy: e.g. organism = "9606" (= taxid of Homo 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 is release = 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").

Value

File path to downloaded CDS file.

See also

getGenome, getProteome, getGFF, getRNA, getRepeatMasker, getAssemblyStats, meta.retrieval, read_cds

Author

Hajk-Georg Drost

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")

}