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Old 04-25-2015, 02:27 PM   #1
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default calculating mutation burden per TCGA sample


in TCGA breast data, I found using expression of genes of interest in the lab, ~120 samples segregate into two groups that have high and low expression of my gene.

I want to summarize that group 1 has higher mutation rate compared to 2nd group. Also I want to summarize the copy number alteration for both groups.

How can I get the summarized value for each groups (perhaps a mean value).

Can I use "mutation count" and 'CNA' columns from Cbioportal clinical sheets.

or Do I have to calculate that per KB of the genome how many mutations are observed?

Appreciate your help.

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