| genRandBioSeqs {kebabs} | R Documentation |
Generate biological sequences with uniform random distribution of alphabet characters.
genRandBioSeqs(seqType = c("DNA", "RNA", "AA"), numSequences, seqLength,
biostring = TRUE, seed)
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 |
seed |
when present the random generator will be seeded with the value passed in this parameter |
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.
When the parameter 'biostring' is set to FALSE the function returns a XStringSet derived class otherwise a BioVector derived class.
Johannes Palme <kebabs@bioinf.jku.at>
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.
## 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)