How to find out out Transmission Probability Matrix

Hi, I have a fixed time scale ,say every hour from 6.00am to 6.00pm. I have three inputs to be observed. I have three states (say 0,1,2) for two of my inputs and two (say 0,1) for the third input. Thus I will get a 18*18 transmission matrix. How can i get the transmission probability matrix connecting the three states, given all the states of all the inputs within the time.? I know the concept to do it manually, but is there any way to find it out in Matlab.? Any help would be greatly appreciated.