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# Builds a matrix of transitions and their probabilities from <markovSimulation>
getTransitionProbabilities <- function(markovSimulation)
{
stopifnot(inherits(markovSimulation,"MarkovSimulation"))
if (is.null(markovSimulation$table))
stop(paste("The supplied simulation result does not contain transition information.",
"Please re-run markovSimulation() with returnTable=TRUE!"))
initialStates <- t(apply(markovSimulation$table$initialStates,2,dec2bin,length(markovSimulation$genes)))
nextStates <- t(apply(markovSimulation$table$nextStates,2,dec2bin,length(markovSimulation$genes)))
idx <- order(apply(initialStates,1,function(x)paste(x,collapse="")))
res <- data.frame(initialStates,nextStates,markovSimulation$table$probabilities)
res <- res[idx,]
rownames(res) <- NULL
colnames(res) <- c(paste("initialState.",markovSimulation$genes,sep=""),
paste("nextState.",markovSimulation$genes,sep=""),
"probability")
return(res)
}
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