biomartr (version 0.5.1)

getCDS: Coding Sequence Retrieval

Description

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, 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"
• db = "ensemblgenomes"

organism

a character string specifying the scientific name of the organism of interest, e.g. organism = "Homo sapiens".

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, meta.retrieval, read_cds

Examples

## Not run: ------------------------------------
# # 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")
# 
## ---------------------------------------------