random_length {FastqCleaner} | R Documentation

## Create a named object with random sequences and qualities

### Description

Create a `ShortReadQ` object with random sequences and qualities

### Usage

    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

### Author(s)

Leandro Roser learoser@gmail.com

### 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

    set.seed(10)
    s2 <- random_seq(slength = 10, swidth = 20,
    prob = c(0.6, 0.1, 0.3, 0))
    s2

[Package FastqCleaner version 1.6.0 Index]