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RNA Sequence Retrieval

Source: R/getRNA.R
getRNA.Rd

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,
  skip_bacteria = TRUE,
  release = NULL,
  assembly_type = "toplevel",
  path = file.path("_ncbi_downloads", "RNA"),
  gunzip = FALSE,
  mute_citation = FALSE
)

Arguments

db

a character string specifying the database from which the genome shall be retrieved:

  • db = "refseq"

  • db = "genbank"

  • db = "ensembl"

organism

Organism selector id, 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 a candidate for downloaded if it isn't marked in the database as either a reference genome or a representative genome. This is helpful if you don't want to allow "partial genomes" etc.

skip_bacteria

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 = FALSE is set then the bacterial summary file will be downloaded.

release

a numeric, the database release version of ENSEMBL (db = "ensembl"). Default is release = NULL meaning that the most recent database version is used. release = 75 would 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.

assembly_type

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

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").

gunzip

a logical, indicating whether or not files should be unzipped.

mute_citation

logical, default FALSE, indicating whether citation message should be muted.

Value

File path to downloaded genome.

Details

Fetching of assembly / sequence data is done by fetching an overview file from metadata of given database:
For NCBI (refseq/genbank):
Internally this function loads the the overview.txt file from NCBI:

refseq: ftp.ncbi.nlm.nih.gov/genomes/refseq/

genbank: ftp.ncbi.nlm.nih.gov/genomes/genbank/

It will then create a directory relative to file type wanted, if you get fasta genomes it will be _ncbi_downloads/genomes' etc. 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.

For ensembl it fetches overview per type from the rest API:

ensembl: https://rest.ensembl.org

See also

Other getBio: getBio(), getCDS(), getCollection(), getGFF(), getGenome(), getProteome()

Other rna: getRNASet(), read_rna()

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# download the RNA of Arabidopsis thaliana from refseq
# and store the corresponding RNA file in '_ncbi_downloads/RNA'
file_path <- getRNA( db       = "refseq",
             organism = "Arabidopsis thaliana",
             path     = file.path("_ncbi_downloads","RNA"))

Ath_RNA <- read_rna(file_path, format = "fasta")
} # }