Hello Everyone,

Has anyone used CN.MOPS for CNV analysis ? If so, how do you get it to recognize your genomic loci coming from separate chromosomes ? I read the paper and it seems the authors have used one simulated data as coming from one long artificial chromosome and the other data set consisted of only the X chromosome. My input data is a read count matrix and I am following the guideline used in the sample data set provided by them with the R package. i,e :

for e.g Chr_2_6225001_6250000, Chr_3_7225001_7250000, etc.

Thank You