Data are data. They exist as discrete elements in computers because (except for signal-level internal voltages and currents in the semiconductors and busses, and the output from soundcards) everything is sampled and therefore discrete by definition.
Functions that process discrete data have z-transforms, while data themselves do not.
However if the objective is to produce a state-space (or transfer function) representation of the system that created the data using the input and output data, then use the System Identification Toolbox functions to identify it. Begin with the iddata function, and proceed from there. Both continuous-time and discrete-time realisations of the system are possible.
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