Create a named object with random sequences and qualities — random_length • FastqCleaner
Description: Create a ShortReadQ object with random sequences and qualities

# Create a named object with random sequences and qualities

`random_length.Rd`

Create a `ShortReadQ` object with random sequences and qualities

    random_length(n, widths, random_widths = TRUE, replace = TRUE,
      len_prob = NULL, seq_prob = c(0.25, 0.25, 0.25, 0.25),
      q_prob = NULL, nuc = c("DNA", "RNA"), qual = NULL,
      encod = c("Sanger", "Illumina1.8", "Illumina1.5", "Illumina1.3",
      "Solexa"), base_name = "s", sep = "_")

## Arguments

n | number of sequences
widths | width of the sequences
random_widths | width must be picked at random from the passed parameter 'widths', considering the value as an interval where any integer can be picked. Default TRUE. Otherwise, widths are picked only from the vector passed.
replace | sample widths with replacement? Default TRUE.
len_prob | vector with probabilities for each width value. Default NULL (equiprobability)
seq_prob | a vector of four probabilities values 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].
q_prob | a vector of range = range(qual), with probabilities to set the frequency of each quality value. Default is equiprobability. If the sum of the probabilities is > 1, the values will be nomalized to the range [0, 1].
nuc | create sequences of DNA (nucleotides = c('A', 'C', 'G', 'T')) or RNA (nucleotides = c('A, 'C', 'G', 'U'))?. Default: 'DNA'
qual | quality range for the sequences. It must be a range included in the selected encoding: 'Sanger' = [0, 40] 'Illumina1.8' = [0, 41] 'Illumina1.5' = [0, 40] 'Illumina1.3' = [3, 40] 'Solexa' = [-5, 40] example: for a range from 20 to 30 in Sanger encoding, pass the argument = c(20, 30)
encod | sequence encoding
base_name | Base name for strings
sep | Character separing base names and the read number. Default: '_'

## Value

`ShortReadQ` 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