Questions for OncoPrint

[김경아(병리학교실)]

To Whom it may concern,

 

I am KyungA Kim at Yonsei Medical University in Korea.

I am so thankful for you to provide a concise and convenient tool, “OncoPrint”.

 

I got several questions during the usage.

It will be a big help for me, program beginner if you give me advices.

 

First question, which category is suitable for “Frameshift Indel” mutation?

There are four mutation categories: missense, inframe, trunc and other.

 

Secondly, do I have to filter out mutations prior to visualize by OncoPrint?

I mean there are same gene mutations but with different more sites and each different values.

Do I have to manually filtering out before Oncoprint?

 

Thirdly, I uploaded my input file around 2000 samples. It stopped and showed the size file is too big.

How can I solve this problem?

 

Thanks for considering my questions!

 

Sincerely,

Kyunga Kim

 

[Tali Mazor]

Hi Kyunga Kim,

Thanks for your kind words.

Frameshift indels are generally considered truncating mutations (trunc).

You do not need to filter out mutations prior to using OncoPrint. If a sample has multiple mutations in the same gene, then the sample will be colored according to the most deleterious event and all mutations will be visible in a tooltip if you hover over the sample/gene box in the OncoPrint.

There is no file size limit, but when the number of genes * the number of samples gets larger than ~100,000, there can be performance issues. Depending on how many genes/mutations are present in those ~2000 samples, you might be running into that problem. I suggest trying with a subset of the data rather than all at once.

-Tali

On Tue, Mar 3, 2020 at 9:47 AM 김경아(병리학교실) <JOY...@yuhs.ac> wrote:

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