I am working with cn.mops for CNV identification from exome data for unpaired samples.
The problem I am facing is, when I used "unpaired" mode, the zero column in Readcounts matrix, but I use sampe samples with paired mode, normalization is done and no error.
The "mode" argument does not refer to whether your samples are "paired" or "unpaired", but to the reads. If you have used a sequencing technology with paired end reads and used a read mapper that aligns paired reads, then your choice should be "paired". Otherwise the correct choice is "unpaired".
This is also the reason why your read count matrix consist only of zeros when you pick the wrong option.
