TaxRec-class: Taxonomic record

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

Taxonomic record

Description

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

Usage

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

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

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

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

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

Arguments

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

Slots

id

Taxonomic ID

scnm

Scientific name

cmnm

Common name

rnk

Rank

lng

Lineage

prnt

Parent

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)
# 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

ropensci/phylotaR documentation built on July 21, 2024, 1:01 a.m.