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, skip_bacteria = TRUE, release = NULL, assembly_type = "toplevel", path = file.path("_ncbi_downloads", "RNA"), gunzip = FALSE, mute_citation = FALSE )
a character string specifying the database from which the genome shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
Organism selector id, 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.
Due to its enormous dataset size (> 700MB as of July 2023), the bacterial summary file will not be loaded by default anymore. If users wish to gain insights for the bacterial kingdom they needs to actively specify
skip_bacteria = FALSE. When
skip_bacteria = FALSEis set then the bacterial summary file will be downloaded.
a numeric, the database release version of ENSEMBL (
db = "ensembl"). Default is
release = NULLmeaning that the most recent database version is used.
release = 75would for human would give the stable GRCh37 release in ensembl. Value must be > 46, since ensembl did not structure their data if the standard format before that.
character, default c("primary_assembly", "toplevel"). Used for ensembl only, specifies the genome assembly type. Searches for both primary and toplevel, and if both are found, uses the first by order (so primary is prioritized by default). The Primary assembly should usually be used if it exists. The "primary assembly" contains all the top-level sequence regions, excluding alternative haplotypes and patches. If the primary assembly file is not present for a species (only defined for standard model organisms), that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: ensembl tutorial
a character string specifying the location (a folder) in which the corresponding CDS file shall be stored. Default is
a logical, indicating whether or not files should be unzipped.
logical, default FALSE, indicating whether citation message should be muted.
Internally this function loads the the overview.txt file from NCBI:
and creates a directory relative to file type, if you get fasta genomes it will be _ncbi_downloads/genomes'. In case the corresponding fasta file already exists within the '_ncbi_downloads/genomes' folder and is accessible within the workspace, no download process will be performed. For other file types the same rule applies.