SeqArc-class: Sequence record archive

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

Description

Multiple sequence records containing sequence data.

Usage

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

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

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

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

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

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

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

Arguments

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

Details

Sequences are stored as raw. Use rawToChar().

Slots

ids

Vector of Sequence Record IDs

nncltds

Vector of sequence lengths

nambgs

Vector of number of ambiguous nucleotides

txids

Vector source txid associated with each sequence

sqs

List of SeqRecs named by ID

See Also

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

Examples

data('aotus')
seqarc <- aotus@sqs
# this is a SeqArc object
# it contains sequence records
show(seqarc)
# you can access its different data slots with @
seqarc@ids     # sequence IDs defined as accession + feature position
seqarc@nncltds # number of nucleotides of all sequences  
seqarc@nambgs  # number of ambiguous nucleotides of all sequences
seqarc@txids   # all the taxonomic IDs for all sequences
seqarc@sqs     # list of all SeqRecs
# access sequence records [[
(seqarc[[seqarc@ids[[1]]]])  # first sequence record
# generate new sequence archives with [
(seqarc[seqarc@ids[1:10]])  # first 10 sequences

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