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, freqs,
  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.

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.

monofreqs

numeric Deprecated. Use freqs instead.

difreqs

numeric Deprecated. Use freqs instead.

trifreqs

numeric Deprecated. Use freqs instead.

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

Pagès 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(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("!@#$ ")


[Package universalmotif version 1.2.1 Index]