Phylota-class: Phylota object

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

Description

Phylota table contains all sequence, cluster and taxonomic information from a phylotaR pipeline run.

Usage

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

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

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

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

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

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

Arguments

x	Phylota object
object	Phylota object
max.level	Maximum level of nesting for str()
...	Further arguments for str()
i	Either sid or cid

Slots

cids

IDs of all clusters

sids

IDs of all sequences

txids

IDs of all taxa

sqs

All sequence records as SeqArc

clstrs

All cluster records as ClstrArc

txdct

Taxonomic dictionary as TaxDict

prnt_id

Parent taxonomic ID

prnt_nm

Parent taxonomic name

See Also

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

Examples

data('aotus')
# this is a Phylota object
# it contains cluster, sequence and taxonomic information from a phylotaR run
show(aotus)
# you can access its different data slots with @
aotus@cids   # cluster IDs
aotus@sids   # sequence IDs
aotus@txids  # taxonomic IDs
aotus@clstrs # clusters archive
aotus@sqs    # sequence archive
aotus@txdct  # taxonomic dictionary
# see all of the available slots
(slotNames(aotus))
# access different sequences and clusters with [[
(aotus[['0']])              # cluster record 0
(aotus[[aotus@sids[[1]]]])  # first sequence record
# get a summary of the whole object
(summary(aotus))
# the above generates a data.frame with information on each cluster:
# ID - unique id in the object
# Type - cluster type
# Seed - most connected sequence
# Parent - MRCA of all represented taxa
# N_taxa - number of NCBI recognised taxa
# N_seqs - number of sequences
# Med_sql - median sequence length
# MAD - Maximum alignment density, values close to 1 indicate all sequences in
#  the cluster have a similar length.
# Definition - most common words (and frequency) in sequence definitions
# Feature - most common feature name (and frequency)

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