R: Generic function to get sequence data

getSequence {seqinr} | R Documentation

## Generic function to get sequence data

### Description

getSequence returns the sequence either as vector of single chararacters or as a single string of multiple characters.

### Usage

    getSequence(object, as.string = FALSE, ...)
    ## S3 method for class 'SeqAcnucWeb'
    getSequence(object, as.string = FALSE, ..., socket = autosocket())

### Arguments

`object` | an object of the class `SeqAcnucWeb` or `SeqFastadna`, or `SeqFastaAA` or `SeqFrag` or a list of these objects, or an object of class `qaw` created by `query`
`as.string` | if TRUE sequences are returned as strings of multiple characters instead of a vector of single characters
`socket` | an object of class `sockconn` connecting to a remote ACNUC database (default is a socket to the last opened database).
`...` | further arguments passed to or from other methods

### Value

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.

### Author(s)

D. Charif, J.R. Lobry, L. Palmeira

### References

`citation("seqinr")`

### See Also

`SeqAcnucWeb`, `SeqFastadna`, `SeqFastaAA`, `SeqFrag`

### Examples

    #
    # List all available methods for getSequence generic function:
    #
       methods(getSequence)
    #
    # 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)

[Package seqinr version 3.4-5 Index]