Your question is potentially very broad in scope, so I'll try to provide a narrow answer. And I'm assuming that by looking at real estate as an investment you mean that you're expecting to profit from periodic cash flows over the time that you will hold the asset.
If that's the case, then the model for valuing investment real estate isn't all that much different in a macro sense than valuing financial assets. The differences that do exist can be accounted for in estimating your discount rate and your final expected cash flow (i.e., the estimated terminal value of the asset).
As you've noted, the primary differences between an investment in real estate and an investment in financial assets are (1) liquidity and (2) transaction costs. For the former you can attempt to quantify the effect of illiquidity by adding a component to the discount rate. In a sense illiquidity is a form of risk, and the extent to which that risk impacts you depends in part on your goals as an investor. But if you wish to try to measure the impact of illiquidity in the general marketplace, you're going to have to get some data. For transaction costs, I should think that you would account for that in your terminal value.
For more information see http://www.amazon.com/Investment-Valuation-Techniques-Determining-Second/dp/0471414883