What do the columns CN and segm.mean represent for the "CN.seg" file?

Question

What do the columns CN and segm.mean represent for the "CN.seg" file?

mbihie opened this issue a year ago · 1 comments

I was hoping to use the CN and segm.mean columns found in the subclone1_CN.seg files from the Intratumoral heterogeneity in Glioblastoma example. I wanted to use them to compare the copy number deletion of 1 type of cancer to another. Could anyone clarify exactly what they mean?

Thank you!

Answer 1 · 2023-10-20T14:16:30.000Z

Hello @mbihie,
segm.mean is the mean CN log ratio of all cells of that subclone in a specific segment of the genome, and CN is the infer integer copy number obtained as explained in the our paper (4 amp 3 Gain 1 Loss 0 Del).

Regards