transition.matrix.di <-
function(di.dfa,con.prob){ #include
n.states<-dim(di.dfa)[1]
states <- rownames(di.dfa)
tr.mat <- matrix(0,nrow=n.states,ncol=n.states)
rownames(tr.mat)<-states
colnames(tr.mat)<-states
givenbase <- gsub("[0123456789]","",states)
for (i in 1:n.states){#for (i in 1:n.states){
for (j in colnames(di.dfa)){
to.st <- di.dfa[states[i],j]
tr.mat[states[i],to.st] <- tr.mat[states[i],to.st]+con.prob[j,givenbase[i]]
}
}
return(tr.mat)
}
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