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sbonisso / clinical_tcga

Library for parsing clinical metadata files from TCGA
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Sample IDs and Clinical features example #1

Open andrewmaltezthomas opened 9 years ago

andrewmaltezthomas commented 9 years ago

Hi Sboniso,

I came across your repository when searching for easy ways to parse TCGA clinical files. However, I don't know exactly what sort of Sample IDs and Clinical features to insert. Could you put in some examples?

Thanks,

Andrew

sbonisso commented 9 years ago

Hi Andrew,

Sorry for the delayed response. I will try to update the repo this weekend with a clear example and better gem instructions. Didn't think anyone would use it, mostly put it up for myself.

To answer your question, the sample IDs you need to give it are 'barcode IDs', e.g., TCGA-4N-A93T-01A. You can see some examples in test/test_clinical_metadata.rb. You can convert from UUIDs to barcode IDs using the convert_tcga_uuid.rb script, which was my use case.

For features these are the strings at the top of the metadata files, e.g., "last_contact_days_to" for a clinical_followup file, or "percent_tumor_nuclei" for a biospecimen_slide type file. Some more examples of these are in the same test/test_clinical_metadata.rb.

Hope this helps.

-Stefano