listGenomes: List All Available Genomes

Description Usage Arguments Details Note Author(s) Examples

View source: R/listGenomes.R

Description

This function retrieves the names of all genomes available on the NCBI ftp:// server and stores the results in a file named 'overview.txt' inside the directory _ncbi_downloads' that is built inside the workspace.

Usage

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listGenomes(db = "refseq", type = "all", subset = NULL, details = FALSE)

Arguments

db

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

type

a character string specifying a potential filter of available genomes. Options are type = "all", type = "kingdom", type = "group", type = "subgroup".

subset

a character string or character vector specifying a subset of type. E.g. if users are interested in retrieving all Eukaryota species, they can specify: type = "kingdom" and subset = "Eukaryota".

details

a boolean value specifying whether only the scientific names of stored genomes shall be returned (details = FALSE) or all information such as organism_name,kingdoms, group, subgroup, file_size_MB, etc.

Details

Internally this function loads the the overview.txt file from NCBI and creates a directory '_ncbi_downloads' in the temdir() folder to store the overview.txt file for future processing. In case the overview.txt file already exists within the '_ncbi_downloads' folder and is accessible within the workspace, no download process will be performed again.

Note

Please note that the ftp:// connection relies on the NCBI or ENSEMBL server and cannot be accurately accessed via a proxy.

Author(s)

Hajk-Georg Drost

Examples

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## Not run: 
# print details for refseq
listGenomes(db = "refseq") 

## End(Not run)

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