PolyDist: Fraction of substitutions by polymorphic site

In VHIRHepatiques/QSutils: Quasispecies Diversity

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)

VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.