Statistically robust approach of assigning presence or absence of Histone peaks

Question

[Saad Khan]

Hi I am looking at orthologus regions and histone modifications around those regions between Human and Mouse. So if I have to make a vector for presence or absence of a histone in a particular region I will overlap it with the orthologus region and based on the size of overlap of the peak and the orthologus region I will consider it a 1 or a 0 based on absence or presence of the histone in the orthologus region. Usually I take a hard threshold but I was wondering if there is a more statistically robust approach to do that.

So my vector would be Histone 1 (h3k4me1) and histone 2 e.t.c in the indices of the vector. I hope I am clear and would appreciate if someone could suggest the best possible way to do that.