create_sequences {universalmotif} | R Documentation |
Create random sequences.
Description
Generate random sequences from any set of characters, represented as
XStringSet
objects.
Usage
create_sequences(alphabet = "DNA", seqnum = 100, seqlen = 100, freqs,
nthreads = 1, rng.seed = sample.int(10000, 1))
Arguments
alphabet |
character(1) One of c('DNA', 'RNA', 'AA') , or a string of
characters to be used as the alphabet.
|
seqnum |
numeric(1) Number of sequences to generate.
|
seqlen |
numeric(1) Length of random sequences.
|
freqs |
numeric A named vector of probabilities. The length of the
vector must be the power of the number of letters in the sequence alphabet.
Probabilities can only be provided for a single size k.
|
nthreads |
numeric(1) Run create_sequences() in parallel with nthreads
threads. nthreads = 0 uses all available threads.
Note that no speed up will occur for jobs with seqnum = 1 .
|
rng.seed |
numeric(1) Set random number generator seed. Since sequence
creation can occur simultaneously in multiple threads using C++, it cannot
communicate with the regular R random number generator state and thus requires
an independent seed. Each individual sequence creation instance is
given the following seed: rng.seed * index . The default is to pick a random
number as chosen by sample() , which effectively is making create_sequences()
dependent on the R RNG state.
|
Value
XStringSet
The returned sequences are unnamed.
Author(s)
Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca
See Also
create_motif()
, shuffle_sequences()
Examples
## Create DNA sequences with slightly increased AT content:
sequences <- create_sequences(freqs = c(A=0.3, C=0.2, G=0.2, T=0.3))
## Create custom sequences:
sequences.QWER <- create_sequences("QWER")
## You can include non-alphabet characters are well, even spaces:
sequences.custom <- create_sequences("!@#$ ")
[Package
universalmotif version 1.12.2
Index]