is.genome.available: Check Genome Availability

Description Usage Arguments Details Value Author(s) Examples

View source: R/is.genome.available.R

Description

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

Usage

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

Arguments

db

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

  • db = "refseq"

  • db = "genbank"

  • db = "ensembl"

  • db = "ensemblgenomes"

  • 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)

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.

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.

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.

Author(s)

Hajk-Georg Drost

Examples

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## 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")

## End(Not run)

biomartr documentation built on July 2, 2018, 1:02 a.m.