phylotaR (version 1.0.0)

SeqArc-class: Sequence record archive

Description

Multiple sequence records containing sequence data.

Usage

# S4 method for SeqArc
as.character(x)
# S4 method for SeqArc
show(object)
# S4 method for SeqArc
print(x)
# S4 method for SeqArc
str(object, max.level = 2L, ...)
# S4 method for SeqArc
summary(object)
# S4 method for SeqArc,character
[[(x, i)
# S4 method for 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

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

Details

Sequences are stored as raw. Use rawToChar().

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

# NOT RUN {
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
# }