Create a DNAStringSet object with random sequences

random_seq(slength, swidth, nuc = c("DNA", "RNA"), prob = c(0.25, 0.25,
  0.25, 0.25))

Arguments

slength

Number of sequences

swidth

Width of the sequences

nuc

Create sequences of DNA (nucleotides = c('A', 'C', 'G', 'T')) or RNA (nucleotides = c('A, 'C', 'G', 'U'))?. Default: 'DNA'

prob

A vector of four probability values used to set the frequency of the nucleotides 'A', 'C', 'G', 'T', for DNA, or 'A', 'C', 'G', 'U', for RNA. For example = c(0.25, 0.25, 0.5, 0). Default is = c(0.25, 0.25, 0.25, 0.25) (equiprobability for the 4 bases). If the sum of the probabilities is > 1, the values will be nomalized to the range [0, 1].

Value

DNAStringSet object

Examples

# For reproducible examples, make a call to set.seed before # running each random function set.seed(10) s1 <- random_seq(slength = 10, swidth = 20) s1
#> A DNAStringSet instance of length 10 #> width seq #> [1] 20 TGGTCCGGTGTTCTGGCGGA #> [2] 20 ATAGGTACAGTCCAGTAATT #> [3] 20 GCCTCCCGCAGACGCTGGGT #> [4] 20 CCGGAATGCCCTTTCTGAGC #> [5] 20 AGCTCCAGCCGTTTGACTTC #> [6] 20 GCGGAAAGTGAACTTAGATT #> [7] 20 CGGTCCTGAAACACGGTACT #> [8] 20 TCCACAGTCAACCCGCCGAC #> [9] 20 TTGGAGAATTTATTAGCCGG #> [10] 20 GCGGTTATTCCCCTAGTGAT
set.seed(10) s2 <- random_seq(slength = 10, swidth = 20, prob = c(0.6, 0.1, 0.3, 0)) s2
#> A DNAStringSet instance of length 10 #> width seq #> [1] 20 AAAGAAAAGAGAAAAAAAAG #> [2] 20 GGGAAGGAGAAAAGAGGCGA #> [3] 20 AAAGAAAAAGACAAAAAAAA #> [4] 20 AAAAGGAAAAAAGAAAACAA #> [5] 20 GAAGAAGAAAAGAAAGAAGA #> [6] 20 AAAACGCAGAGGAAGCAGGG #> [7] 20 AAAAAAGAGCGAGAAAGGAA #> [8] 20 GAACAGAGACGAAAAAAACA #> [9] 20 GAAAGAGCGAAGGGCAAAAA #> [10] 20 AAAAAGGGGAAAAAGAAAGG