genRandBioSeqs {kebabs} | R Documentation

## Generate Random Biological Sequences

### Description

Generate biological sequences with uniform random distribution of alphabet characters.

### Usage

    genRandBioSeqs(seqType = c("DNA", "RNA", "AA"), numSequences, seqLength,
      biostring = TRUE, seed)

### Arguments

`seqType` | defines the type of sequence as DNA, RNA or AA and the underlying alphabet. Default="DNA"
`numSequences` | single numeric value which specifies the number of sequences that should be generated.
`seqLength` | either a single numeric value or a numeric vector of length 'numSequences' which gives the length of the sequences to be generated.
`biostring` | if `TRUE` the sequences will be generated in XStringSet format otherwise as BioVector derived class. Default=TRUE
`seed` | when present the random generator will be seeded with the value passed in this parameter

### Details

The function generates a set of sequences with uniform distribution of alphabet characters and returns it as XStringSet or BioVector dependent on the parameter `biostring`.

### Value

When the parameter 'biostring' is set to FALSE the function returns a XStringSet derived class otherwise a BioVector derived class.

### Author(s)

Johannes Palme <kebabs@bioinf.jku.at>

### References

http://www.bioinf.jku.at/software/kebabs
J. Palme, S. Hochreiter, and U. Bodenhofer (2015) KeBABS: an R package for kernel-based analysis of biological sequences. Bioinformatics, 31(15):2574-2576, 2015. DOI: 10.1093/bioinformatics/btv176.

### Examples

    ## generate a set of AA sequences of fixed length as AAStringSet
    aaseqs <- genRandBioSeqs("AA", 100, 1000, biostring=TRUE)

    ## show AA sequence set
    aaseqs

    ## Not run:
    ## generate a set of "DNA" sequences as DNAStringSet with uniformly
    ## distributed lengths between 1500 and 3000 bases
    seqLength <- runif(300, min=1500, max=3500)
    dnaseqs <- genRandBioSeqs("DNA", 100, seqLength, biostring=TRUE)

    ## show DNA sequence set
    dnaseqs

    ## End(Not run)

[Package kebabs version 1.14.0 Index]