The Observed number of CpG patterns in a window is simply the count of the number of times a 'C' is found followed immediately by a 'G'.
The Expected number of CpG patterns is calculated for each window as the number of CpG dinucleotides you would expect to see in that window based on the frequency of C's and G's in that window. Thus, the Expected frequency of CpG's in a window is calculated as the number of 'C's in the window multiplied by the number of 'G's in the window, divided by the window length.
Expected = (number of C's * number of G's) / window length