FAD: Functional attribute diversity
In VHIRHepatiques/QSutils: Quasispecies Diversity
FAD R Documentation
Functional attribute diversity
Description
Computes the Functional Attribute Diversity as the sum of elements in
the pairwise distance matrix.
Usage
FAD(dst)
Arguments
dst
A "dist" object or a symmetrical matrix with pairwise distances.
Value
A value that corresponds to the Functional Attribute Diversity.
The sum of matrix elements.
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.
See Also
DNA.dist
Examples
# Create the object.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
# Compute the DNA distance matrix.
dst <- DNA.dist(lst$hseqs,model="N")
FAD(dst)
VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| FAD | R Documentation |
Functional attribute diversity
Description
Computes the Functional Attribute Diversity as the sum of elements in the pairwise distance matrix.
Usage
FAD(dst)
Arguments
dst |
A "dist" object or a symmetrical matrix with pairwise distances. |
Value
A value that corresponds to the Functional Attribute Diversity. The sum of matrix elements.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
References
Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.
See Also
DNA.dist
Examples
# Create the object.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
# Compute the DNA distance matrix.
dst <- DNA.dist(lst$hseqs,model="N")
FAD(dst)
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.