Main retrieval function for RNA sequences of an organism of interest. By specifying the scientific name of an organism of interest the corresponding fasta-file storing the RNA information for the organism of interest can be downloaded and stored locally. RNA files can be retrieved from several databases.
Usage
getRNA(
db = "refseq",
organism,
reference = FALSE,
release = NULL,
path = file.path("_ncbi_downloads", "RNA")
)
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.- 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","RNA")
.