Genomic Data Commons hosts a gene-wise copy number summary for each cancer, which has genes as rows and samples as columns. The column headings are aliquot UUIDs. How may these be matched to other data types, such as a MAF file of SNVs which contains TCGA barcodes as the sample identifier?
Thanks for your question. I've added support for this in TCGAutils
library(TCGAutils) UUIDtoBarcode("d85d8a17-8aea-49d3-8a03-8f13141c163b", "aliquot_ids") #> analytes.aliquots.aliquot_id analytes.aliquots.submitter_id #> 13 d85d8a17-8aea-49d3-8a03-8f13141c163b TCGA-CV-5443-01A-01D-1510-01
Created on 2019-07-17 by the reprex package (v0.3.0)
In TCGAbiolinks, when reading the copy number data we use the GDC API to map the aliquot id to barcode: https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1182-L1211