DNAseqtest (version 1.0)

Pt: Transition Probability Function

Description

This function calculates the transition probability function for a process during a period of time.

Usage

Pt(S, Pi, t)

Arguments

S

a 4 x 4 symmetric matrix

Pi

a diagonal matrix containing the stationary distribution for the process

t

a period of time describing the length of the process

Value

Details

This function needs the 4 x 4 symmetric matrix S, II and the process length t in order to find the transition probability over that process, where $P_{ij}(t)$ is the probability that the ith nucleotide changes to the j-th nucleotide during the period of t.

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

Smatrix

Examples

Pi<-diag(c(.1,.1,.1,.7)) 
S<-Smatrix(c(.3,.3,.3,.3,.3,.3),diag(Pi))
t<-1
p<-Pt(S, Pi, t)
p