RNA Sequence RetrievalSource:
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.
getRNA( db = "refseq", organism, reference = FALSE, release = NULL, path = file.path("_ncbi_downloads", "RNA") )
a character string specifying the database from which the genome shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
there are three options to characterize an organism:
scientific name: e.g.
organism = "Homo sapiens"
database specific accession identifier: e.g.
organism = "GCF_000001405.37"(= NCBI RefSeq identifier for
taxonomic identifier from NCBI Taxonomy: e.g.
organism = "9606"(= taxid of
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.
the database release version of ENSEMBL (
db = "ensembl"). Default is
release = NULLmeaning that the most recent database version is used.
a character string specifying the location (a folder) in which the corresponding CDS file shall be stored. Default is