R: split a sequence into sub-sequences

splitseq {seqinr} | R Documentation

## split a sequence into sub-sequences

### Description

Split a sequence into sub-sequences of 3 (the default size) with no overlap between the sub-sequences.

### Usage

    splitseq(seq, frame = 0, word = 3)

### Arguments

`seq` | a vector of chars
`frame` | an integer (0, 1, 2) giving the starting position to split the sequence
`word` | an integer giving the size of the sub-sequences

### Value

This function returns a vector which contains the sub-sequences.

### Author(s)

J.R. Lobry

### References

`citation("seqinr")`

### See Also

`split`

### Examples

    cds <- s2c("aacgttgcaggtcgctcgctacgtagctactgttt")
    #
    # To obtain the codon sequence in frame 0:
    #
    stopifnot(identical(splitseq(cds),
      c("aac", "gtt", "gca", "ggt", "cgc", "tcg", "cta", "cgt", "agc", "tac", "tgt")))
    #
    # Show the effect of frame and word with a ten char sequence:
    #
    (tenchar <- s2c("1234567890"))
    splitseq(tenchar, frame = 0)
    splitseq(tenchar, frame = 1)
    splitseq(tenchar, frame = 2)
    splitseq(tenchar, frame = 0, word = 2)
    splitseq(tenchar, frame = 0, word = 1)

[Package seqinr version 3.4-5 Index]