cn.MOPS fails with 'missing value where TRUE/FALSE needed'
I managed to track down what was producing this error. The problem was that my bed file only had one segment for chromosome chrUn_gl000228. However, the cn.MOPS method relies on normalizing read counts across multiple segments for each chromosome. Since this chromosome only had a single segment, the exomecn.mops(X) was failing. 

So, either remove the single segment from the bed file, or use a bed file that has at least 2 segments on each chromosome. I created a fake segment on chrUn_gl000228 and confirmed that the program worked as expected and didn't throw any errors.