Pt {DNAseqtest} | R Documentation |
This function calculates the transition probability function for a process during a period of time.
Pt(S, Pi, t)
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 |
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.
A 4 x 4 matrix containing the transition probabilities for a process.
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.
Smatrix
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