This function checks the availability of a given genome on the NBCI servers specified as scientific name.
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 forHomo sapiens
)by
taxonomic identifier from NCBI Taxonomy
: e.g.organism = "9606"
(= taxid ofHomo sapiens
)
- 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.
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.
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")
}