How to interpret the Copy Number from pseudocount depmap portal file?
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4 months ago
flalom • 0

Hi there, Do you know how to interpret the Copy Number (CN) file from the depmap portal: CCLE_gene_cn.csv. 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.

My question is: how do I convert this file into useful information such as HOMDEL and AMP?

This is how 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


PS I cross-posted this on bioinformatics.stackexchange as well, here

cancer depmap cell-lines CN • 352 views