SegSites: Compute the number of segregating sites
In VHIRHepatiques/QSutils: Quasispecies Diversity
SegSites R Documentation
Compute the number of segregating sites
Description
Computes the number of segregating (polymorphic) sites in a given alignment.
That is, the number of sites with more than a single nucleotide or amino acid
in the alignment.
Usage
SegSites(seqs)
Arguments
seqs
DNAStringSet or AAStringSet with the haplotype sequences.
Value
A value corresponding to the number of polymorphic sites.
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
# Create the object.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
SegSites(lst$hseqs)
VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.
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| SegSites | R Documentation |
Compute the number of segregating sites
Description
Computes the number of segregating (polymorphic) sites in a given alignment. That is, the number of sites with more than a single nucleotide or amino acid in the alignment.
Usage
SegSites(seqs)
Arguments
seqs |
DNAStringSet or AAStringSet with the haplotype sequences. |
Value
A value corresponding to the number of polymorphic sites.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
References
Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.
Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.
See Also
ReadAmplSeqs
Examples
# Create the object.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
SegSites(lst$hseqs)
R Package Documentation
Browse R Packages
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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