PolyDist: Fraction of substitutions by polymorphic site
In QSutils: Quasispecies Diversity
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
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
1
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
Examples
1
2
3
4
5
6
# 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$nr)
QSutils documentation built on Nov. 8, 2020, 7:42 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
Computes the fraction of substitutions at each polymorphic site. The wild-type
base is taken as the most abundant at each site, taking into account the
weights, w.
Usage
1 |
Arguments
seqs |
DNAStringSet or AAStringSet with the haplotype sequences. |
w |
An optional numeric vector with the haplotype counts. When |
Value
Vector of numbers corresponding to the fraction of substitutions at polymorphic
sites. Note that the wild type also depends on w.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
References
Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.
Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.
See Also
Examples
1 2 3 4 5 6 | # Load haplotype alignment with abundances.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
PolyDist(lst$hseqs)
PolyDist(lst$hseqs,lst$nr)
|
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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