I am hoping to get some clarification on how the copy number values are calculated for Y-chromosome genes. Given that the copy number value is calculated as log2(relative CN + 1), what is the relative CN for a normal copy number of a Y-chromosome gene? Does it account for the fact there is only 1 Y-chromosome and set the normal relative CN to 1/1, or is the normal relative CN 1/2 in a diploid cell? Thanks!
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