TotalMutations {QSutils} | R Documentation

## Number of Mutations

### Description

`TotalMutations` computes the number of mutations in the alignment.

### Usage

    TotalMutations(hseqs,w)

### Arguments

`hseqs` | DNAStringSet or AAStringSet with the haplotype sequences.
`w` | An optional numeric vector with the haplotype counts used to compute the total number of mutations in the population, that is, taking into account haplotype abundances. When `w` is NULL, a vector of ones is taken as default.

### Value

A value corresponding to the number of mutations. Note that the wild-type is decided taking `w` into account.

### 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

`SegSites`

### Examples

    # Create the object.
    filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
    lst <- ReadAmplSeqs(filepath,type="DNA")

    TotalMutations(lst$hseqs)
    TotalMutations(lst$hseqs,lst$nr)

[Package QSutils version 1.2.0 Index]