Distance: Paralinear Distances

In DNAseqtest: Generating and Testing DNA Sequences

Description

This function calculates the paralinear distance between K matched DNA sequences.

Usage

Distance(F4)

Arguments

F4	a 4^K array containing the joint distribution array F(t) or the observed array N

Details

This function calculates the paralinear distances between K matched DNA sequences, depending on the joint distribution array for these K sequences or on the observed divergence array N.

Value

A K x K symmetric matrix distances between the K sequences

References

Faisal Ababneh, Lars S Jermiin, Chunsheng Ma, John Robinson (2006). Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22(10), 1225-1231.

See Also

gn2, gn, Fmatrix, Ntml

Examples

merge2<-matrix(c(-1,-4,-3,2,-2,-5,1,3), 4, 2)
theta<-c(rep(.25,3), rep(.25,3), rep(.25,3), c(.2,.35,.79,.01,.93,.47), 3,.1,.5,.8)
F1<-gn(theta,merge2)
dn<-Distance(F1)
dn

Example output

      [,1]  [,2] [,3]  [,4]  [,5]
[1,] 0.000 0.825  6.6 5.500 5.500
[2,] 0.825 0.000  6.6 5.500 5.500
[3,] 6.600 6.600  0.0 5.500 5.500
[4,] 5.500 5.500  5.5 0.000 1.375
[5,] 5.500 5.500  5.5 1.375 0.000

DNAseqtest documentation built on May 1, 2019, 9:51 p.m.