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waldronlab / TCGAutils

Toolbox package for organizing and working with TCGA data
https://bioconductor.org/packages/TCGAutils
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Inquiry Regarding TCGA Barcode Identification with TCGAutils #34

Closed Sarigenes closed 4 months ago

Sarigenes commented 4 months ago

Issue Description: Struggling with identifying TCGA barcodes for samples in a manifest file downloaded from the 2020 GDC Data Portal. This is crucial for distinguishing between tumor and normal samples.

Steps Taken: Attempted "UUID to TCGA barcode" function from TCGAutils, resulting in "See help("GDC-defunct")" error. Tried 'UUIDhistory', which only provided version information without updates (see below).

Current Situation: Uncertain how to obtain TCGA barcodes for accurate sample classification from the manifest file.

Request for Assistance: Seeking guidance on efficiently identifying TCGA barcodes for samples in the manifest file.

Additional Information with Manifest File: Download Date: 2020 Code used:

uuids <- c("11b29aeb-57c7-48dd-b2fc-3190d4ea4d39",
           "15c6062d-ae1e-4d9b-ba92-11faad1f727a")

UUIDtoBarcode(uuids, from_type = "file_id")

Output:

The 'legacy' argument is defunct.
See help("GDC-defunct")

Code used:

UUIDhistory("657e1896-01c2-4e91-a0a1-aa112a382e43")

Output:

uuid version file_change release_date data_release
657e1896-01c2-4e91-a0a1-aa112a382e43       1    released   2018-08-23         12.0

Your assistance in resolving this issue is greatly appreciated!

LiNk-NY commented 4 months ago

Hi @Sarigenes

I wasn't able to reproduce the error with Bioconductor 3.18 or 3.19. You may be looking for legacy files that no longer exist in the GDC.

I don't remember when the legacy argument was defunct but it looks like you may have an old Bioconductor installation. Given that this package and GenomicDataCommons use APIs, it is strongly recommended that you update your installation. You should be using Bioconductor version 3.18 or greater.

Best regards, Marcel

Sarigenes commented 4 months ago

Hi @LiNk-NY,

Thank you very much for the information, noted well.

Have a great day ahead.

LiNk-NY commented 4 months ago

@Sarigenes FWIW, I searched the GDC for these files at e.g., https://portal.gdc.cancer.gov/v1/files/11b29aeb-57c7-48dd-b2fc-3190d4ea4d39 and it looks like they were removed and no information is provided.