You cannot pause a running program. The closest you can get is to put in a breakpoint or a conditional breakpoint before you start running the program.
But possibly you meant something else by "from GUI"; above I was answering about the MATLAB interface to run and debug programs.
If you are constructing a GUI that is starting a routine in a callback, then there is no mechanism in MATLAB to force that routine to pause when the user clicks something (or uses the keyboard.) It is possible, however, to write the routine so that it asks whether the user would like it to pause, or so that it notices that the user has changed values in a user interface and use the new values. To do this, the routine needs to use drawnow() to give the user interface an opportunity to do pending actions, and the routine needs to get() values from the handles in order to receive the updated values. For example,
for x = 1 : 1000
drawnow()
a = str2double(get(handles.editbox_a, 'String'));
b = str2double(get(handles.editbox_b, 'String'));
y(x) = a * x + b * x^2;
end