TCGA Primary sample

Question

[abdulrehman19427]

I downloaded LGG data from TCGA in MAF format. I want to proceed with the primary site data. I could not find any primary samples. Is there any primary sample in TCGA project? If yes which column of MAF file show primary samples? Should I use the sample barcode to find primary samples?

[abdulrehman19427]

Thank u so much for your help My issue is completely resolved with your help

[Kevin Blighe]

Sounds good.

Answer 1

[Kevin Blighe]

You may find this code, courtesy of Seán Davis, of use for identifying the metastatic samples: A: TCGA metastatic samples

You can adapt it for your own needs.

[abdulrehman19427]

thanks for your help but i want to find TCGA primary samples

[Kevin Blighe]

All that you need to do is:

library(GenomicDataCommons)

response <- cases() %>%
  filter(~ project.project_id=='TCGA-LGG' & samples.sample_type=='Primary Tumor') %>%
  GenomicDataCommons::select(c(default_fields(cases()), 'samples.sample_type')) %>%
  response_all()

Then parse the results object, response. There does not appear to be any metastatic samples for TCGA-GLL.

[abdulrehman19427]

Hi Kevin i downloaded the metastatic samples of LGG that was 0. Then i downloaded the BRCA metastasis sample that was 7. But the sample id is in form of "TCGA-BH-A18V" but i need only 7 sample IDs in form of "TCGA-VM-A8CB-01A-11D-A36O-08"

[Kevin Blighe]

The full TCGA barcodes should be in the response object, no? Type str(response) to take a look inside it.