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)

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.

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 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)

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


[Package universalmotif version 1.6.4 Index]