Access to Putative arm-level copy-number from GISTIC in TCGA

[DELFOUR OLIVIER]

Dear Colleagues,

 

Still time to wish you an happy new year 😃

 

I have a question for cbioportal gurus: I would like to download all Arm-level CNA for TCGA Bladder Cancer (BLCA) indication.

I have read that it could be possible to do so by using the oncoprinter, but it didn’t work.

 

I can see that the query works well  since I can see Putative arm-level copy-number from GISTIC and chromosome arms in oncoprint web page. But, when I download the file, the data for Arm are not present in the file.

 

Can you help me ?

 

Many thanks,

 

Olivier

 

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[Tali Mazor]

Hi Olivier,

If you want to download the entire set of arm-level data for a study, the easiest way is probably to download directly from the cBioPortal DataHub, where you can find all the data that we upload into the public portal. For arm-level data for TCGA BLCA, you can download the 'data_armlevel_cna.txt' file here: https://github.com/cBioPortal/datahub/tree/master/public/blca_tcga_pan_can_atlas_2018

-Tali

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[DELFOUR OLIVIER]

Hi Tali,

Many thanks. Very usefull.

Best regards,

Olivier

 

 

De : Tali Mazor <tma...@ds.dfci.harvard.edu>
Envoyé : lundi 24 janvier 2022 20:34
À : DELFOUR OLIVIER <olivier...@pierre-fabre.com>
Cc : cbiop...@googlegroups.com
Objet : Re: [cbioportal] Access to Putative arm-level copy-number from GISTIC in TCGA

 

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