Random Sequence Generator Based on a Multinomial Model

Source: R/randomSeqs.R

This function computes random sequences based on the alphabet and word length of an input sequence based on a multinomial model.

randomSeqs(seq, sample_size)

Arguments

seq

a character vector storing a sequence as string for which random sequences shall be computed.
sample_size

a numeric value specifying the number of random sequences that shall be returned.

Value

a character vector of length sample_size storing the random string objects.

Details

This function enables you to create a test statistic for sequence comparisons that are based on a multinomial model assumption. When spexifying the sample_size argument a vector of strings of corresponding sample_size is being returned.

The random strings returned by randomSeqs have the same word length and are drawn from the same alphabet as the input sequence.

See also

evalAlignment, randSeqDistr

Examples

# a nucleotide example
seq_example <- "ACCTGGAATTC"
randomSeqs(seq = seq_example, sample_size = 10)
#>  [1] "TCGCGCACTCG" "AAGGCGTAGAG" "CCCGCCCGCTA" "GAGTTGTACCT" "TTAGTGGCTAC"
#>  [6] "TTAGAGCTAGT" "TTACAATTAGA" "CTCCGTTATCA" "CTTGCGATTCA" "TATCCGCTGGT"

# a protein example
seq_example <- "NPPAAM"
randomSeqs(seq = seq_example, sample_size = 10)
#>  [1] "MAAANP" "AAMAPA" "PNAAAA" "MPNNPM" "PANANA" "ANNMPA" "PNANAA" "ANPAPN"
#>  [9] "NMPPAP" "MPNPNP"