Hi, you implied that you have already obtained the data. So, please proceed with your analysis.
You will have to develop some code that identifies deletion of the entire chromosomal arms. You can create rules that define whether an arm is deleted or not.
By the way: within the LGG (Lower Grade Glioma) TCGA cohort are already-identified oligodendroglioma samples (n=191). Please search the associated clinical data for LGG. The file is the BCR Biotab file, nationwidechildrens.org_clinical_patient_lgg.txt, available at the GDC Data portal.
Lower Grade Glioma (LGG) is already classified into
I was analysing these samples just a few weeks ago.