For CNV analysis in targeted NGS data, I am trying to run the tutorial of ExomeDepth library. In the step of building the most appropriate reference set as following:
my.choice <- select.reference.set (test.counts = my.test,reference.counts = my.reference.set, bin.length = (my.counts.dafr$end - my.counts.dafr$start))
I received the following error:
"Optimization of the choice of aggregate reference set, this process can take some time It looks like the test samples has only 0 bins with 2 or more reads. The coverage is too small to perform any meaningful inference so no likelihood will be computed."
Any recommendation, please? Thanks for the help.