biomartr (version 0.5.1)

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(organism, details = FALSE, db = "refseq")

Arguments

organism

a character string specifying the scientific name of the organism of interest, e.g. organism = "Homo 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.

db

a character string specifying the database for which genome availability shall be checked, e.g. db = "refseq",db = "genbank", db = "ensembl", db = "ensemblgenomes", or db = "all".

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

## Not run: ------------------------------------
# # 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")
## ---------------------------------------------