Taxonomic dictionary contains a taxonomic tree and NCBI taxonomy data for all taxonomic IDs.
Usage
# S4 method for TaxRec
as.character(x)
# S4 method for TaxRec
show(object)
# S4 method for TaxRec
print(x)
# S4 method for TaxRec
str(object, max.level = 2L, ...)
# S4 method for TaxRec
summary(object)Arguments
- x
TaxRecobject- object
TaxRecobject- max.level
Maximum level of nesting for str()
- ...
Further arguments for str()
See also
Other run-public:
ClstrArc-class,
ClstrRec-class,
Phylota-class,
SeqArc-class,
SeqRec-class,
TaxDict-class,
clusters2_run(),
clusters_run(),
parameters_reset(),
reset(),
restart(),
run(),
setup(),
taxise_run()
Examples
data('aotus')
taxrec <- aotus@txdct@recs[[aotus@txdct@txids[[1]]]]
# this is a TaxRec object
# it contains NCBI's taxonomic information for a single node
show(taxrec)
#> TaxRec [id 2688256 (unclassified Aotus (in: primates))]
# you can access its different data slots with @
taxrec@id # taxonomic ID
#> [1] "2688256"
taxrec@scnm # scientific name
#> [1] "unclassified Aotus (in: primates)"
taxrec@cmnm # common name, '' if none
#> [1] ""
taxrec@rnk # rank
#> [1] "no rank"
taxrec@lng # lineage information: list of IDs and ranks
#> $ids
#> [1] "131567" "2759" "33154" "33208" "6072" "33213" "33511"
#> [8] "7711" "89593" "7742" "7776" "117570" "117571" "8287"
#> [15] "1338369" "32523" "32524" "40674" "32525" "9347" "1437010"
#> [22] "314146" "9443" "376913" "314293" "9479" "376918" "9504"
#> [29] "2688256"
#>
#> $rnks
#> [1] "no rank" "superkingdom" "clade" "kingdom" "clade"
#> [6] "clade" "clade" "phylum" "subphylum" "clade"
#> [11] "clade" "clade" "clade" "superclass" "clade"
#> [16] "clade" "clade" "class" "clade" "clade"
#> [21] "clade" "superorder" "order" "suborder" "infraorder"
#> [26] "parvorder" "family" "genus" "no rank"
#>
taxrec@prnt # parent ID
#> [1] "9504"