FAD: Functional attribute diversity
In QSutils: Quasispecies Diversity
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
Computes the Functional Attribute Diversity as the sum of elements in
the pairwise distance matrix.
Usage
1
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
Examples
1
2
3
4
5
6
7
8
# 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$hseqs,model="N")
FAD(dst)
QSutils documentation built on Nov. 8, 2020, 7:42 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
Computes the Functional Attribute Diversity as the sum of elements in the pairwise distance matrix.
Usage
1 | FAD(dst)
|
Arguments
dst |
A "dist" object or a symmetrical matrix with pairwise distances. |
Value
A value that corresponds to the Functional Attribute Diversity. The sum of matrix elements.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
References
Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.
See Also
Examples
1 2 3 4 5 6 7 8 | # Create the object.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
# Compute the DNA distance matrix.
dst <- DNA.dist(lst$hseqs,model="N")
FAD(dst)
|
R Package Documentation
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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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