Adding feature to exclude samples

[Mohamed Alshalalfa]

Hi,

I am a big fan and user of cbioportal!! THANK YOU for this amazing tool!!

I have one comment. I am trying to do genomic comparison between TP53mut vs TP53 no mut. The only way I found now is to select TP53mut samples and create one group and select all other samples and create a new group. I am wondering if there is a way to add "exclude" tab in the mutations graph to be able to exclude samples with particular mutations.

Thank you!

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Mohammed Alshalalfa, PhD

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[Tali Mazor]

Hi Mohamed,

Thanks for the kind words!

We don't have that feature available in study view - within study view, the only option is to filter to TP53 mutant samples and then use the Custom Selection menu to select the currently unselected samples, which it sounds like is what you are doing.

Another option is to run a query for TP53 (or, if you want only TP53 mutations, use OQL to limit your query, eg query for 'TP53: MUT' ). When you run a query, the Comparison tab provides the same group comparison functionality as if you define groups in study view, but the groups default to altered samples (those with TP53 mutation) and unaltered samples (those without TP53 mutations).

-Tali

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[Mohamed Alshalalfa]

Thanks a lot Tali!

I figured out how to do it after seeing this video on youtube. Custom selection was the key !

cBioPortal Webinar 4: Group Comparison