FAD: Functional attribute 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

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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

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# 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 May 8, 2019, 1:44 p.m.