ClstrRec-class: Cluster record

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

Description

Cluster record contains all information on a cluster.

Usage

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

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

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

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

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

Arguments

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

Slots

id

Cluster ID, integer

sids

Sequence IDs

nsqs

Number of sequences

txids

Source txids for sequences

ntx

Number of taxa

typ

Cluster type: direct, subtree or merged

seed

Seed sequence ID

prnt

Parent taxonomic ID

See Also

Other run-public: ClstrArc-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')
clstrrec <- aotus@clstrs@clstrs[[1]]
# this is a ClstrRec object
# it contains cluster information
show(clstrrec)
# you can access its different data slots with @
clstrrec@id     # cluster id
clstrrec@sids   # sequence IDs
clstrrec@nsqs   # number of sequences
clstrrec@txids  # taxonomic IDs of sequences
clstrrec@ntx    # number unique taxonomic IDs
clstrrec@typ    # cluster type: merged, subtree, direct or paraphyly
clstrrec@prnt   # MRCA of all taxa
clstrrec@seed   # most inter-connected sequence

phylotaR documentation built on May 1, 2019, 9:26 p.m.