TaxDict-class: Taxonomic record dictionary

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Taxonomic record dictionary

Description

Taxonomic dictionary contains a taxonomic tree and NCBI taxonomy data for all taxonomic IDs.

Usage

## S4 method for signature 'TaxDict'
as.character(x)

## S4 method for signature 'TaxDict'
show(object)

## S4 method for signature 'TaxDict'
print(x)

## S4 method for signature 'TaxDict'
str(object, max.level = 2L, ...)

## S4 method for signature 'TaxDict'
summary(object)

Arguments

x	TaxDict object
object	TaxDict object
max.level	Maximum level of nesting for str()
...	Further arguments for str()

Slots

txids

Taxonomic IDs of taxon records

recs

Environment of records

prnt

Parent taxonomic ID

txtr

Taxonomic tree

See Also

Other run-public: ClstrArc-class, ClstrRec-class, Phylota-class, SeqArc-class, SeqRec-class, TaxRec-class, clusters2_run(), clusters_run(), parameters_reset(), reset(), restart(), run(), setup(), taxise_run()

Examples

data('aotus')
txdct <- aotus@txdct
# this is a TaxDict object
# it contains taxonomic information, including records and tree
show(txdct)
# you can access its different data slots with @
txdct@txids  # taxonomic IDs
txdct@recs   # taxonomic records environment
txdct@txtr   # taxonomic tree
txdct@prnt   # MRCA
# access any record through the records environment
txdct@recs[[txdct@txids[[1]]]]
# for interacting with the taxonomic tree, see the treeman package
summary(txdct@txtr)

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.