TotalMutations: Number of Mutations

In VHIRHepatiques/QSutils: Quasispecies Diversity

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)

VHIRHepatiques/QSutils documentation built on April 12, 2024, 12:25 p.m.