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List number of available genomes in each taxonomic group

Source: R/listGroups.R
listGroups.Rd

Users can retrieve the available number of sequenced genomes per group. Only available for db = "refseq" and db = "genbank".

Usage

listGroups(db = "refseq", kingdom = "all", details = FALSE)

Arguments

db

a character string specifying the database for which genome availability shall be checked. Available options are:

  • db = "refseq"

  • db = "genbank"

kingdom

a kingdom specification retrieved by getKingdoms.

details

shall all species corresponding to the specified kingdom be returned? Default is details = FALSE.

See also

listGenomes, is.genome.available, listKingdoms

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# retrieve a list of available kingdoms
getKingdoms()
# [1] "archaea"              "bacteria"             "fungi"                "invertebrate"         "plant"               
# [6] "protozoa"             "vertebrate_mammalian" "vertebrate_other"     "viral"  
# example for refseq
listGroups(db = "refseq")
# example for genbank
listGroups(db = "genbank")
### in case groups should be specified by kingdom
# first, retrieve available kingdom names
listKingdoms()
# now we choose kingdom "bacteria"
listGroups(db = "refseq", kingdom = "bacteria")
# or
listGroups(db = "genbank", kingdom = "bacteria")
} # }