Steps to process CNV level 3 files from TCGA database

Question

[Na Sed]

I am trying to process the CNV files downloaded from TCGA database. Actually, I am not familiar with this type of data and it is the first time I am working on CNV data.

Before, with help of guys, I could extract the name of genes for each region. I was surprised when I found out many genes for each segment (I am not biologist!!).

Currently, I want to make a matrix like [genes x segment_mean], but I don't know what should I do with these data. I searched about it in google as well as Biostar but I could not find any useful information. I appreciate if anyone help and introduce some texts, as well.