Entering edit mode
Hi,
I have a list of fileuuids obtained from TCGA portal. I am trying to use GenomicDataCommons package to extract sample type(whether normal or tumor) and TCGA barcodes associated with input fileuuids. From the manual I can get to this
resp = cases() %>% filter(~ project.project_id=='TCGA-LUAD') %>%
GenomicDataCommons::select(c(default_fields(cases()),'samples.sample_type')) %>%
response_all()
Can someone guide me how to extract TCGA barcode and sample type from list of uuids?
Thanks
HI Kevin, I used Sean's code and got the barcodes. How can I infer tumor|normal from them? For example if I have these barcodes:
Thanks
Ah, for that, please take a look here: https://www.biostars.org/p/313063/
Hi Kevin Blighe Sean Davis , the link is really helpful to do the translation, and I found TCGAutils is helpful too.
But, I got a question. As below, "afe6dd5c-a32e-4ba8-a9b5-154b27a9513b" is the file_id. How about the prefix in the bam file or bai file? What id it is?