PolyDist {QSutils} | R Documentation

## Fraction of substitutions by polymorphic site

### Description

Computes the fraction of substitutions at each polymorphic site. The wild-type base is taken as the most abundant at each site, taking into account the weights, `w`.

### Usage

    PolyDist(seqs,w=NULL)

### Arguments

`seqs` | DNAStringSet or AAStringSet with the haplotype sequences.
`w` | An optional numeric vector with the haplotype counts. When `w` is NULL, the same weight is given to each haplotype.

### Value

Vector of numbers corresponding to the fraction of substitutions at polymorphic sites. Note that the wild type also depends on `w`.

### Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

### References

Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.

Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.

### See Also

`ReadAmplSeqs`

### Examples

    # Load haplotype alignment with abundances.
    filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
    lst <- ReadAmplSeqs(filepath,type="DNA")

    PolyDist(lst$hseqs)
    PolyDist(lst$hseqs,lst$nr)

[Package QSutils version 1.12.0 Index]