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waldronlab / TCGAutils

Toolbox package for organizing and working with TCGA data
https://bioconductor.org/packages/TCGAutils
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TCGAtranslateID not working? #8

Closed simomounir closed 6 years ago

simomounir commented 6 years ago

Hi all,

I found your package an it happened to be useful since I want to convert some TCGA barcodes to UUID. It worked once but then it did not want to work again even if I did not change the input.

Trying to run this now: TCGAtranslateID(TCGAbarcode("TCGA-44-6147-11A-01R-1858-07"), type="file_id")

but I get:

Warning message: In TCGAtranslateID2(TCGAbarcode("TCGA-44-6147-11A-01R-1858-07"), : No identifier data returned

What could be the problem?

Thanks

LiNk-NY commented 6 years ago

Hi Mohamed, @simomounir

I've started looking into this. The GDC API is quite a challenge to figure out. I've looked at alternatives. For example, using the GenomicDataCommons package to associate files with TCGA barcodes but it also is a bit difficult to get that type of information. There is no standard query to translate a UUID to a barcode since UUIDs can be assigned to files, patients, and samples.

I will be asking the GDC package maintainer for some insights.

Regards, Marcel

LiNk-NY commented 6 years ago

Hi Mohamed, @simomounir

This should be resolved now. Please let me know if you encounter other issues.

Best regards, Marcel