Phylota-class | R Documentation |
Phylota table contains all sequence, cluster and taxonomic information from a phylotaR pipeline run.
## 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]]
x |
|
object |
|
max.level |
Maximum level of nesting for str() |
... |
Further arguments for str() |
i |
Either sid or cid |
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
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()
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)
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