i tried to get treatment information from TCGA-COAD and TCGA-READ data, but all attempts failed.
I downloaded the harmonized, FPKM, clinical and transcriptome profiling data but couldn't find any suitable information about the treatment of the cases.
When looking at the GDC homepage, under the clinical data table I found suitable treatmant items as treatment_type: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/clinical-data-harmonization, but I have no clue how I could get them!??
Here is my code:
library(TCGAbiolinks) # Getting clinical data #--- # XML format: clin.queryR <- GDCquery(project="TCGA-READ", data.category="Clinical") GDCdownload(clin.queryR, method="client") clinicalR <- GDCprepare_clinic(clin.queryR, clinical.info="patient")
I tried all the other clinical.info options too, but I didn't find the treatment_type information. Can you please help me how I could get the treatment_type information? Thanks a lot.