How to interpret the Copy Number from pseudocount depmap portal file?

Question

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How do I convert the Copy Number (CN) file into useful information such as HOMDEL and AMP?

This is an already normalized file with pseudo count + 1. In this file there are values from 0 to 1 for each cancer cell line, in wide format.

I have already looked at the forum post about the file, but it's not helpful for me.

This is what the file looks like:

,DDX11L1 (100287102),WASH7P (653635),FAM138A (645520),OR4F5 (79501)
ACH-000621,1.0166833616923812,1.0166833616923812,1.0166833616923812,1.0166833616923812
ACH-002512,2.9659871795507433,2.9659871795507433,2.9659871795507433,2.9659871795507433
ACH-001188,0.9881267634909964,0.9881267634909964,0.9881267634909964,0.9881267634909964
ACH-000471,0.8053837915961594,0.8053837915961594,0.8053837915961594,0.8053837915961594

Thank you for your help

Answer 1

I'm not familiar with this file structure, but have you looked at the forum post about relative copy number linked to in the FAQ?

Since we do not have matched normals, the output is a “copy ratio” or relative copy number. It is relative to the rest of the genome for that cell line. E.g. if the cell line is tetraploid we would not be able to see it from the relative copy number. These values are reported as log2(relative CN + 1) in the portal.