R: Class for sub-sequences

SeqFrag {seqinr} | R Documentation

## Class for sub-sequences

### Description

`as.SeqFrag` is called by all methods of `getFrag`, but not directly by the users. It creates an object sequence of class `SeqFrag`.

### Usage

     as.SeqFrag(object, begin, end, name)
     is.SeqFrag(object)

### Arguments

`object` | an object sequence of class `seqFastadna`, `seqFastaAA`, `seqAcnucWeb` or `seqFrag`
`begin` | the first base of the fragment to get
`end` | the last base of the fragment to get
`name` | the name of the sequence

### Value

`as.SeqFrag` returns a biological sequence with the following attributes:

`seqMother` | the name of the sequence from which the sequence comes
`begin` | the position of the first base of the fragment on the mother sequence
`end` | the position of the last base of the fragment on the mother sequence
`class` | `SeqFrag` which is the classfor sub-sequence

`is.SeqFrag` returns TRUE if the object is of class Seqfrag.

### Author(s)

D. Charif, J.R. Lobry

### References

`citation("seqinr")`

### See Also

`getFrag`, `getLength`, `getName`, `getSequence`, `getTrans`

### Examples

     s <- read.fasta(file = system.file("sequences/malM.fasta", package = "seqinr"))
     getFrag(s[[1]], 1, 10)

[Package seqinr version 3.4-5 Index]