SeqRec-class: Sequence record

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

Description

Sequence record contains sequence data.

Usage

## 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)

Arguments

x	SeqRec object
object	SeqRec object
max.level	Maximum level of nesting for str()
...	Further arguments for str()

Details

Sequence is stored as raw. Use rawToChar().

Slots

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

See Also

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

Examples

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))

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