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zheins avatar zheins commented on August 21, 2024 1

@pieterlukasse @sandertan - We generate that via our internal importing pipelines. I'll add it to the files.

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pieterlukasse avatar pieterlukasse commented on August 21, 2024

Notify: @n1zea144 @zheins : just something I noticed today, but I could be wrong about whether it is missing in datahub (maybe you recently added it). Please let me know.

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sandertan avatar sandertan commented on August 21, 2024

When the study is downloaded from cbioportal.org, the datahub version is downloaded which misses CANCER_TYPE_DETAILED in sample/patient data. Would be cool to have it included!

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sandertan avatar sandertan commented on August 21, 2024

@zheins Could you check that the correct attribute is used to fill this column? This is from brca_tcga, it seems to miss the information from the public portal:
screen shot 2017-04-12 at 16 33 51

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pieterlukasse avatar pieterlukasse commented on August 21, 2024

@sandertan @zheins I checked this on the public portal again and what @sandertan observes there seems to be correct. The only difference is that "undefined" is called "NA" in study view. When you click "Customize histogram" you will see the other cancer types. They don't appear on the plot because the samples labelled with these cancer types just don't have mutations in TP53. I found another gene where they do have mutations, and it works as expected. See screenshot below:

image

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pieterlukasse avatar pieterlukasse commented on August 21, 2024

just tested it locally on newly downloaded dataset and it works as expected 👍

Closing this issue.

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