the threshold about wgs_somatic_cnv_per_gene data
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zihaoxingstudy1 commented
hello, i see the wgs_somatic_cnv_per_gene data in gbm are continuous data. I want to know how to determine the threshold and define which ranges belong to copy number amplification and copy number deletion
caleb-lindgren commented
In the endometrial cancer flagship paper, they recommend using a cutoff of 0.2 for the log ratio CNV data. Anything over +0.2 would be a copy number amplification, and anything below -0.2 would be a copy number deletion.