TotalMutations: Number of Mutations
In QSutils: Quasispecies Diversity
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
View source: R/TotalMutations.R
Description
TotalMutations computes the number of mutations in the alignment.
Usage
1
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
Examples
1
2
3
4
5
6
# 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$nr)
QSutils documentation built on Nov. 8, 2020, 7:42 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
View source: R/TotalMutations.R
Description
TotalMutations computes the number of mutations in the alignment.
Usage
1 | TotalMutations(hseqs,w)
|
Arguments
hseqs |
DNAStringSet or AAStringSet with the haplotype sequences. |
w |
An optional numeric vector with the haplotype counts used to compute the
total number of mutations in the population, that is, taking into account
haplotype abundances. When |
Value
A value corresponding to the number of mutations. Note that the wild-type is
decided taking w into account.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
References
Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.
Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.
See Also
Examples
1 2 3 4 5 6 | # Create the object.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
TotalMutations(lst$hseqs)
TotalMutations(lst$hseqs,lst$nr)
|
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