Hi,

I'm trying to make a treatment chronology for patients in the TCGA-BRCA database and this rapidly became a big mess... I'm using TCGAbiolinks on R.

I've managed to find the start/stop days after diagnosis for drugs and radiation therapy beginning/ending through clinical info ("clinical_drug_brca", "clinical_radiation_brca"). I've also managed to find the kind of surgery received by certain patients ("clinical_patient_brca"), but when looking for the days when said surgery was done, I can't find them anywhere. Here is the code to find the tables:

query.Clin <- GDCquery(project = "TCGA-BRCA", 
                   data.category = "Clinical",
                   data.type = "Clinical Supplement", 
                   data.format = "BCR Biotab")
GDCdownload(query.Clin, directory = "Clin.data")
Clin.data <- GDCprepare_clinic(query.Clin, directory = "Clin.data") #list of all the clinical tables

I've somehow managed to find a table for samples collection that have a little bit of info about certain surgeries and the day they were made, but not all of them are described ("ssf_tumor_samples_brca"). Here is the code to find that table:

query.Biospe <- GDCquery(project = "TCGA-BRCA", 
              data.category = "Biospecimen",
              data.type = "Biospecimen Supplement", 
              data.format = "BCR Biotab")
GDCdownload(query.Biospe, directory = "Biospe.data")
Biospe.data <- GDCprepare(query.Biospe, directory = "Biospe.data") #list of all the biospecimen tables

Does anybody know where to find the surgery dates? I'm really confused as to how those infos are spread in the database...