Fmatrix {DNAseqtest} R Documentation

Joint Distribution for Two Matched Sequences

Description

This function calculates the joint distribution function for two edge tree.

Usage

Fmatrix(t1, t2, f0, Sx2, Sy2, Pix, Piy)

Arguments

 t1 represents the length from the tree root to the first node t2 represents the length from the tree root to the second node f0 the initial distribution for the four nucleotides Sx2 a 4 x 4 symmetric matrix related to the first edge Sy2 a 4 x 4 symmetric matrix related to the second edge Pix a diagonal matrix for the stationary distribution of the first edge Piy a diagonal matrix for the stationary distribution of the second edge

Details

This function calculates the joint distribution function for a two edge tree with different edge lengths, stationary distributions and differentS matrices.

Value

A 4 x 4 matrix containing the joint edges

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.

gn, Smatrix

Examples

f0<-c(.25,.25,.25,.25)
Pi1<-diag(c(.2,.2,.2,.4))
Pi2<-diag(c(.1,.1,.1,.7))
S1<-Smatrix(c(.2,.2,.2,.2,.2,.2),diag(Pi1))
S2<-Smatrix(c(.3,.3,.3,.3,.3,.3),diag(Pi2))
fm<-Fmatrix(1, .5, f0, S1, S2, Pi1, Pi2)
fm


[Package DNAseqtest version 1.0 Index]