Smatrix: Symmetric Matrix S

Description Usage Arguments Details Value References See Also Examples

Description

This function calculates the symmetric matrix S.

Usage

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Smatrix(s, pix)

Arguments

s

a vector of variables containing the six free parameters in the S matrix

pix

a vector giving the stationary probabilities for the four nucleotides A, C, G and T

Details

This function calculates the matrix S, which we used to calculate the rate matrix R.

Value

A 4 x 4 symmetric matrix

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

Pt, Fmatrix, gn ,gn2

Examples

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s<-c(.1,.2,.3,.4,.5,.6)
pi<-c(.1,.1,.1,.7)
sm<-Smatrix(s, pi)
sm

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