Question about cbioportal filters

[Roy Khalife]

Hello,

I hope all is well.

I know there are ways to filter if someone has a pik3ca mutation on cbioportal, but is there a way to filter everyone who does NOT have a PIK3CA mutation?

Thanks,

Roy

Roy Khalife, MS

Research Associate

Protean BioDiagnostics Inc.

roy.k...@proteanbiodx.com

[Nikolaus Schultz]

Hi Roy,

There is currently no way to do this directly in the study view (although we should consider adding that functionality). You can, however, run a query from the study view, e.g. for just PIK3CA mutation in samples with mutation data. In the Results view, switch to the Download tab and copy or download the “Unaltered samples”. You can paste those back into the study view under “Custom selection”. 

I hope this is helpful.

Niki.

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[de Bruijn, Ino]

Hi Roy,

 

To add: there is a way to do it in the Study View as well, but it only works for simple cases (like no PIK3CA mutation). You can select “PIK3CA mutant” cases from the study view. And then click on “custom selection” followed by “currently unselected”. Then click “filter to listed samples”. This gets you the negation of your selection

 

Just wanted to mention this alternative method

 

Hope that helps!

 

Best wishes,

Ino

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Nikolaus Schultz <nsch...@gmail.com>
Date: Friday, December 8, 2023 at 8:17 AM
To: Roy Khalife <roy.k...@proteanbiodx.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: [EXTERNAL] Re: [cbioportal] Question about cbioportal filters

Hi Roy, There is currently no way to do this directly in the study view (although we should consider adding that functionality). You can, however, run a query from the study view, e. g. for just PIK3CA mutation in samples with mutation data. 

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/8CFD3AA9-9625-42AE-A65A-646FE09B5BA8%40gmail.com.

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[Roy Khalife]

Hello,

Thanks for both these responses - worked like a charm!

Have a great rest of the week,

Roy

Roy Khalife, MS

Research Associate

Protean BioDiagnostics Inc.

roy.k...@proteanbiodx.com

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From: de Bruijn, Ino <debr...@mskcc.org>
Sent: Friday, December 8, 2023 2:30 PM
To: Nikolaus Schultz <nsch...@gmail.com>; Roy Khalife <roy.k...@proteanbiodx.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] Question about cbioportal filters

 

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