create_sequences: Create random sequences.
In bjmt/universalmotif: Import, Modify, and Export Motifs with R

create_sequences

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

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("!@#$ ")

bjmt/universalmotif documentation built on Nov. 16, 2024, 7:38 a.m.