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…
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