ClstrArc-class: Cluster record archive

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

Cluster record archive

Description

Multiple cluster records.

Usage

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

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

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

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

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

## S4 method for signature 'ClstrArc,character'
x[[i]]

## S4 method for signature 'ClstrArc,character,missing,missing'
x[i, j, ..., drop = TRUE]

Arguments

x	ClstrArc object
object	ClstrArc object
max.level	Maximum level of nesting for str()
...	Further arguments for str()
i	cid(s)
j	Unused
drop	Unused

Slots

ids

Vector of cluster record IDs

clstrs

List of ClstrArc named by ID

See Also

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

Examples

data('aotus')
clstrarc <- aotus@clstrs
# this is a ClstrArc object
# it contains cluster records
show(clstrarc)
# you can access its different data slots with @
clstrarc@ids     # unique cluster ID
clstrarc@clstrs  # list of cluster records
# access cluster records [[
(clstrarc[[clstrarc@ids[[1]]]])  # first cluster record
# generate new cluster archives with [
(clstrarc[clstrarc@ids[1:10]])  # first 10 clusters

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