DNAseqtest (version 1.0)

Fmatrix: 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

Value

Details

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

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

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