I have some data on Copy Number Variation (SNP chip) for a population of samples.
In particular, I have a set of samples (considered as cases) which display a specific disease phenotype, and another set (considered as controls) which do not. The cases have not a matched-control. All the controls are taken as a random sample from the population that does not present the disease.
For both cases and controls I have the copy number of some regions. How can I compute the copy number change in cases, such as in GDC?
Should I use (as described in the previously linked page):
performing tangent normalization, which subtracts variation that is found in a set of normal samples
and do you know of any tool to perform this computation?
The data I have is formatted in this way:
Sample_ID chrom start end CN Sample11 19 11991477 12133823 1 Sample11 2 52260564 52431658 1 Sample12 7 5721757 5896192 3 Sample13 10 2269963 2473585 3