Generic function to get sequence data
getSequence returns the sequence either as vector of single chararacters or as a single string of multiple characters.
getSequence(object, as.string = FALSE, ...) ## S3 method for class 'SeqAcnucWeb' getSequence(object, as.string = FALSE, ..., socket = autosocket())
object |
an object of the class |
as.string |
if TRUE sequences are returned as strings of multiple characters instead of a vector of single characters |
socket |
an object of class |
... |
further arguments passed to or from other methods |
For a single sequence an object of class character containing the characters
of the sequence, either of length 1 when as.string is TRUE, or of the length
of the sequence when as.string is FALSE. For many sequences, a list of these.
D. Charif, J.R. Lobry, L. Palmeira
citation("seqinr")
#
# List all available methods for getSequence generic function:
#
methods(getSequence)
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# SeqAcnucWeb class example:
#
## Not run: # Need internet connection
choosebank("emblTP")
fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
getSequence(fc$req[[1]])
getSequence(fc$req[[1]], as.string = TRUE)
closebank()
## End(Not run)
#
# SeqFastaAA class example:
#
aafile <- system.file("sequences/seqAA.fasta", package = "seqinr")
sfaa <- read.fasta(aafile, seqtype = "AA")
getSequence(sfaa[[1]])
getSequence(sfaa[[1]], as.string = TRUE)
#
# SeqFastadna class example:
#
dnafile <- system.file("sequences/someORF.fsa", package = "seqinr")
sfdna <- read.fasta(file = dnafile)
getSequence(sfdna[[1]])
getSequence(sfdna[[1]], as.string = TRUE)
#
# SeqFrag class example:
#
sfrag <- getFrag(object = sfdna[[1]], begin = 1, end = 10)
getSequence(sfrag)
getSequence(sfrag, as.string = TRUE)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.