randomSeq {GeneR}R Documentation

Create random sequence

Description

Function randomSeq creates a random sequence from a distribution of nulcleotides, of poly-nucleotides. A real composition of nucleotides can be use from function compoSeq, with param p=TRUE.

ShuffleSeq creates a sequence while assembling at random specific number of each nucleotides (or poly-nucleotides). These number of nucleotide can be provided by function compoSeq, with param p=FALSE: it is then a re-assemblage of all nucleotides (or tri-nucleotides, or poly-nucleotides) of a real sequence.

Usage

randomSeq(prob = c(0.25, 0.25, 0.25, 0.25, 0), letters = c("T", "C",
"A", "G", "N"), n )
shuffleSeq(count,letters=c("T","C","A","G","N"))

Arguments

prob

A vector of probability weights for obtaining the elements of the vector being sampled or a result from compoSeq function (with option p=TRUE.

count

A vector of number of repetitions for each letters (or bi-tri nucleotides, must be of same length as letters) or a result from compoSeq function (with option p=FALSE).

letters

Letters (or bi-tri nucleotides) to be sampled

n

Integer giving the number of items to choose.

Value

A character string (sequence) or NULL.

Author(s)

A. Lucas

See Also

compoSeq

Examples

## Set seed of your choice (not requiered)
set.seed(3)

####  ----  RANDOMSEQ  ----
## Create a sequence of size 30, GC rich
randomSeq(prob = c(0.20, 0.30, 0.20, 0.30), letters = c("T", "C","A", "G"), n = 30)
## [1] "CTGGAACCGAGGGGTTCATCCCCCCAGTGA"

## use with bi-nucleotides
randomSeq(prob=rep(0.0625,16),letters = c("TT","TC","TA","TG","CT","CC","CA","CG","AT","AC","AA","AG","GT","GC","GA","GG"),n=10)
## [1] "CGCATGATCCCAGGCTAACT"

####  ----  SHUFFLESEQ  ----
## Create a sequence with 7 T, 3 C and A, and 4 G.
shuffleSeq(count=c(7,3,3,4,0),letters=c("T","C","A","G","N"))
## [1] "TATCTTTTGTCGGACGA"

## Same with bi-nucleotides
shuffleSeq(count=c(rep(4,4),rep(2,4),rep(1,4),rep(0,4)),letters = c("TT","TC","TA","TG","CT","CC","CA","CG","AT","AC","AA","AG","GT","GC","GA","GG"))
## [1] "TCTTTCCATTCCTTCTAGTGTACCCGTATACGTGTCTGTGTACTTCAACAACTTAT"


## From a real sequence:
seqNcbi("BY608190",file="BY608190.fa")
readFasta("BY608190.fa")

## create a random sequence from a real tri-nucleotides distribution
## Size of sequence will be 10*3.
randomSeq(compoSeq(wsize=3,p=TRUE),n=10)

## re assemble real tri-nucleotides of a real sequence
shuffleSeq(compoSeq(wsize=3,from=1,to=30,p=FALSE))



[Package GeneR version 2.24.0 Index]