biomartr (version 1.0.7)

is.genome.available: Check Genome Availability

Description

This function checks the availability of a given genome on the NBCI servers specified as scientific name.

Usage

is.genome.available(
  db = "refseq",
  organism,
  skip_bacteria = TRUE,
  details = FALSE
)

Value

a logical value specifing whether or not the genome of the input organism is available. In case details = TRUE only a character string specifying the genome details is being returned.

Arguments

db

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

• db = "refseq"

• db = "genbank"

• db = "ensembl"

• db = "uniprot"

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 for Homo sapiens)

• by taxonomic identifier from NCBI Taxonomy: e.g. organism = "9606" (= taxid of Homo sapiens)

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.

details

a logical value specifying whether or not details on genome size, kingdom, etc. shall be printed to the console intead of a boolean value.

Author

Hajk-Georg Drost

Details

Internally this function calls the listGenomes function to detect all available genomes and checks whether or not the specified organism is available for download.

Examples

if (FALSE) {
# checking whether the Homo sapiens genome is stored on NCBI
is.genome.available(organism = "Homo sapiens", db = "refseq")

# and printing details
is.genome.available(organism = "Homo sapiens", db = "refseq", details = TRUE)

# checking whether the Homo sapiens genome is stored on ENSEMBL
is.genome.available(organism = "Homo sapiens", db = "ensembl")

# and printing details
is.genome.available(organism = "Homo sapiens",
                    details = TRUE,
                    db = "ensembl")
}