random_length: Create a named object with random sequences and qualities

In FastqCleaner: A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

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 [e-mail]

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

FastqCleaner documentation built on Nov. 8, 2020, 5:05 p.m.