SeqRec-class | R Documentation |
Sequence record contains sequence data.
## S4 method for signature 'SeqRec'
as.character(x)
## S4 method for signature 'SeqRec'
show(object)
## S4 method for signature 'SeqRec'
print(x)
## S4 method for signature 'SeqRec'
str(object, max.level = 2L, ...)
## S4 method for signature 'SeqRec'
summary(object)
x |
|
object |
|
max.level |
Maximum level of nesting for str() |
... |
Further arguments for str() |
Sequence is stored as raw. Use rawToChar().
id
Unique ID
nm
Best-guess sequence name
accssn
Accession
vrsn
Accession version
url
URL
txid
Taxonomic ID of source taxon
orgnsm
Scientific name of source taxon
sq
Sequence
dfln
Definition line
ml_typ
Molecule type, e.g. DNA
rec_typ
Record type: Whole or feature
nncltds
Number of nucleotides
nambgs
Number of ambiguous nucleotides
pambgs
Proportion of ambiguous nucleotides
gcr
GC ratio
age
Number of days between sequence upload and running pipeline
Other run-public:
ClstrArc-class
,
ClstrRec-class
,
Phylota-class
,
SeqArc-class
,
TaxDict-class
,
TaxRec-class
,
clusters2_run()
,
clusters_run()
,
parameters_reset()
,
reset()
,
restart()
,
run()
,
setup()
,
taxise_run()
data('aotus')
seqrec <- aotus@sqs@sqs[[1]]
# this is a SeqRec object
# it contains sequence records
show(seqrec)
# you can access its different data slots with @
seqrec@id # sequence ID, accession + feature location
seqrec@nm # feature name, '' if none
seqrec@accssn # accession
seqrec@vrsn # accession version
seqrec@url # NCBI GenBank URL
seqrec@txid # Taxonomic ID
seqrec@orgnsm # free-text organism name
seqrec@sq # sequence, in raw format
seqrec@dfln # sequence definition
seqrec@ml_typ # molecule type
seqrec@rec_typ # whole record or feature
seqrec@nncltds # sequence length
seqrec@nambgs # number of non-ATCGs
seqrec@pambgs # proportion of non-ATCGs
seqrec@gcr # GC-ratio
seqrec@age # days since being added to GenBank
# get the sequence like so....
(rawToChar(seqrec@sq))
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