shuffle_sequences {universalmotif} | R Documentation

## Shuffle input sequences.

### Description

Given a set of input sequences, shuffle the letters within those sequences with any k-let size.

### Usage

    shuffle_sequences(sequences, k = 1, method = "euler", nthreads = 1,
      rng.seed = sample.int(10000, 1), window = FALSE, window.size = 0.1,
      window.overlap = 0.01)

### Arguments

`sequences` | `XStringSet` Set of sequences to shuffle. Works with any set of characters.
`k` | `numeric(1)` K-let size.
`method` | `character(1)` One of `c('euler', 'markov', 'linear')`. Only relevant if `k > 1`. See details.
`nthreads` | `numeric(1)` Run `shuffle_sequences()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads. Note that no speed up will occur for jobs with only a single sequence.
`rng.seed` | `numeric(1)` Set random number generator seed. Since shuffling 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 in an `XStringSet` object will be given the following seed: `rng.seed * index`. The default is to pick a random number as chosen by `sample()`, which effectively is making `shuffle_sequences()` dependent on the R RNG state.
`window` | `logical(1)` Shuffle sequences iteratively over windows instead of all at once.
`window.size` | `numeric(1)` Window size. Can be a fraction less than one, or an integer representing the actual window size.
`window.overlap` | `numeric(1)` Overlap between windows. Can be a fraction less than one, or an integer representing the actual overlap size.

### Details

If `method = 'markov'`, then the Markov model is used to generate sequences which will maintain (on average) the k-let frequencies. Please note that this method is not a 'true' shuffling, and for short sequences (e.g. <100bp) this can result in slightly more dissimilar sequences versus true shuffling. See Fitch (1983) for a discussion on the topic.

If `method = 'euler'`, then the sequence shuffling method proposed by Altschul and Erickson (1985) is used. As opposed to the 'markov' method, this one preserves exact k-let frequencies. This is done by creating a k-let edge graph, then following a random Eulerian walk through the graph. Not all walks will use up all available letters however, so the cycle-popping algorithm proposed by Propp and Wilson (1998) is used to find a random Eulerian path. A side effect of using this method is that the starting and ending sequence letters will remain unshuffled.

If `method = 'linear'`, then the input sequences are split linearly every `k` letters. For example, for `k = 3` 'ACAGATAGACCC' becomes 'ACA GAT AGA CCC'; after which these `3`-lets are shuffled randomly.

Do note however, that the `method` parameter is only relevant for `k > 1`. For `k = 1`, a simple shuffling is performed using the `shuffle` function from the C++ standard library.

### Value

`XStringSet` The input sequences will be returned with identical names and lengths.

### Author(s)

Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca

### References

Altschul SF, Erickson BW (1985). “Significance of Nucleotide Sequence Alignments: A Method for Random Sequence Permutation That Preserves Dinucleotide and Codon Usage.” Molecular Biology and Evolution, 2, 526-538.

Fitch WM (1983). “Random sequences.” Journal of Molecular Biology, 163, 171-176.

Propp JG, Wilson DW (1998). “How to get a perfectly random sample from a generic markov chain and generate a random spanning tree of a directed graph.” Journal of Algorithms, 27, 170-217.

### See Also

`create_sequences()`, `scan_sequences()`, `enrich_motifs()`, `shuffle_motifs()`

### Examples

    if (R.Version()$arch != "i386") {
    sequences <- create_sequences()
    sequences.shuffled <- shuffle_sequences(sequences, k = 2)
    }

[Package universalmotif version 1.10.2 Index]