Matlab compiler

Hi all!
We have a problem that we hope you can help us solve.
We wish to compile (to obtain a .exe) a program in Matlab that we have programmed (Matlab R2009b, compiler 4.6). This program internally generates a .m file which must be later called inside the program.
This .m file does not exist until the program has run, hence we cannot compile it along with the program.
Can you help us compiling the .m file?
Or is there a way to call this function in the .exe?
Thank you.

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