Description Usage Arguments Slots See Also Examples
Taxonomic dictionary contains a taxonomic tree and NCBI taxonomy data for all taxonomic IDs.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
x |
|
object |
|
max.level |
Maximum level of nesting for str() |
... |
Further arguments for str() |
id
Taxonomic ID
scnm
Scientific name
cmnm
Common name
rnk
Rank
lng
Lineage
prnt
Parent
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
1 2 3 4 5 6 7 8 9 10 11 12 | 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)
# you can access its different data slots with @
taxrec@id # taxonomic ID
taxrec@scnm # scientific name
taxrec@cmnm # common name, '' if none
taxrec@rnk # rank
taxrec@lng # lineage information: list of IDs and ranks
taxrec@prnt # parent ID
|
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