utils-sequence {universalmotif} | R Documentation

## Sequence-related utility functions.

### Description

Sequence-related utility functions.

### Usage

    count_klets(string, k = 1, alph)

    get_klets(lets, k = 1)

    mask_seqs(seqs, pattern, RC = FALSE, letter = "-")

    shuffle_string(string, k = 1, method = c("euler", "linear", "markov"),
      rng.seed = sample.int(10000, 1))

### Arguments

`string` | `character(1)` A length one character vector.
`k` | `integer(1)` K-let size.
`alph` | `character(1)` A single character string with the desired sequence alphabet. If missing, finds the unique letters in the string.
`lets` | `character` A character vector where each element will be considered a single unit.
`seqs` | `XStringSet` Sequences to mask. Cannot be `BStringSet`.
`pattern` | `character(1)` Pattern to mask.
`RC` | `logical(1)` Whether to mask the reverse complement of the pattern.
`letter` | `character(1)` Character to use for masking.
`method` | `character(1)` Shuffling method. One of `c("euler", "linear", "markov")`. See `shuffle_sequences()`.
`rng.seed` | `numeric(1)` Set random number generator seed. Since shuffling in `shuffle_sequences()` 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. Since `shuffle_string()` uses the same underlying code as `shuffle_sequences()`, it also requires a separate seed even if it is run in serial.

### Value

For `count_klets()`: A `data.frame` with columns `lets` and `counts`.

For `get_klets()`: A `character` vector of k-lets.

For `mask_seqs()`: The masked `XStringSet` object.

For `shuffle_string()`: A single `character` string.

### Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

### See Also

`create_sequences()`, `shuffle_sequences()`

### Examples

    #######################################################################
    ## count_klets
    ## Count k-lets for any string of characters
    count_klets("GCAAATGTACGCAGGGCCGA", k = 2)
    ## The default 'k' value (1) counts individual letters
    count_klets("GCAAATGTACGCAGGGCCGA")

    #######################################################################
    ## get_klets
    ## Generate all possible k-lets for a set of characters
    get_klets(c("A", "C", "G", "T"), 3)
    ## Note that each element in 'lets' is considered a single unit;
    ## see:
    get_klets(c("AA", "B"), k = 2)

    #######################################################################
    ## mask_seqs
    ## Mask repetitive seqeuences
    data(ArabidopsisPromoters)
    mask_seqs(ArabidopsisPromoters, "AAAAAA")

    #######################################################################
    ## shuffle_string
    ## Shuffle any string of characters
    shuffle_string("ASDADASDASDASD", k = 2)

[Package universalmotif version 1.8.5 Index]