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,
      monofreqs, difreqs, trifreqs, progress = FALSE, BP = FALSE)

### 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.
`monofreqs` | `numeric` Alphabet frequencies to use. If missing assumes uniform frequencies. Not used if `difreq` or `trifreq` are input.
`difreqs` | `numeric` Dinucleotide frequencies. DNA/RNA only. Must be a named numeric vector of length 16.
`trifreqs` | `numeric` Trinucleotide frequencies. DNA/RNA only. Must be a named numeric vector of length 64.
`progress` | `logical(1)` Show progress. Not recommended if `BP = TRUE`.
`BP` | `logical(1)` Allows the use of BiocParallel within `create_sequences()`. See `BiocParallel::register()` to change the default backend. Setting `BP = TRUE` is only recommended for large jobs (such as `create_sequences(seqlen=100000,seqnum=100000)`). Furthermore, the behaviour of `progress = TRUE` is changed if `BP = TRUE`; the default BiocParallel progress bar will be shown (which unfortunately is much less informative).

### Value

`XStringSet` The returned sequences are unnamed.

### Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

### References

PagÃƒÂ¨s H, Aboyoun P, Gentleman R, DebRoy S (2018). Biostrings: Efficient manipulation of biological strings. R package version 2.48.0.

### See Also

`create_motif()`, `shuffle_sequences()`

### Examples

    ## create DNA sequences with slightly increased AT content:
    sequences <- create_sequences(monofreqs = c(0.3, 0.2, 0.2, 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 1.0.22 Index]