dinucleotides {seqinr} | R Documentation

## Statistical over- and under- representation of dinucleotides in a sequence

### Description

These two functions compute two different types of statistics for the measure of statistical dinculeotide over- and under-representation : the rho statistic, and the z-score, each computed for all 16 dinucleotides.

### Usage

    rho(sequence)
    zscore(sequence, simulations = NULL, modele, ... )

### Arguments

`sequence` | A nucleic acids sequence
`simulations` | If `NULL`, analytical solution is computed when available (models `base` and {codon}). Otherwise, it should be the number of permutations for the z-score computation
`modele` | A string of characters describing the model chosen for the random generation
`...` | Optional parameters for specific model permutations are passed on to `permutation` function.

### Details

The `rho` statistic, as presented in Karlin S., Cardon LR. (1994), can be computed on each of the 16 dinucleotides. It is the frequence of dinucleotide xy divided by the product of frequencies of nucleotide x and nucleotide y. It is equal to 1.00 when dinucleotide xy is formed by pure chance, and it is superior (respectively inferior) to 1.00 when dinucleotide xy is over- (respectively under-) represented.

The `zscore` statistic, as presented in Palmeira, L., Guéguen, L. and Lobry JR. (in prep.). The statistic is the normalization of the `rho` statistic by its expectation and variance according to a given random sequence generation model, and follows the standard normal distribution. This statistic can be computed with several models (cf. `permutation` for the description of each of the models). We provide analytical calculus for two of them: the `base` permutations model and the `codon` permutations model.

The `base` model allows for random sequence generation by shuffling (with/without replacement) of all bases in the sequence. Analytical computation is available for this model.

The `position` model allows for random sequence generation by shuffling (with/without replacement) of bases within their position in the codon (bases in position I, II or III stay in position I, II or III in the new sequence.

The `codon` model allows for random sequence generation by shuffling (with/without replacement) of codons. Analytical computation is available for this model.

The `syncodon` model allows for random sequence generation by shuffling (with/without replacement) of synonymous codons.

### Value

a table containing the computed statistic for each dinucleotide

### Author(s)

Leonor Palmeira

### References

`citation("seqinr")`

Karlin S. and Cardon LR. (1994) Computational DNA sequence analysis. Annu Rev Microbiol, 48, 619–54.

Palmeira, L., Guéguen, L. and Lobry JR. (in prep) UV-targeted dinucleotides are not depleted in light-exposed Prokaryotic genomes.

### See Also

`permutation`

### Examples

    sequence=sample(s2c('acgt'),6000,rep=TRUE)
    rho(sequence)
    zscore(sequence,modele='base')
    zscore(sequence,modele='codon')
    zscore(sequence,1000,modele='syncodon')

[Package seqinr version 1.0-4 Index]