SeqArc-class | R Documentation |
Multiple sequence records containing sequence data.
## 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]
x |
|
object |
|
max.level |
Maximum level of nesting for str() |
... |
Further arguments for str() |
i |
sid(s) |
j |
Unused |
drop |
Unused |
Sequences are stored as raw. Use rawToChar().
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
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()
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
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