I should start by saying I'm a complete undergrad beginner in Bioinformatics, just recently learning key basic concepts of programming and data structure. I'm trying to extract data from TCGA in order to compare mutational status in two genes across a cohort of cancer patients. Our hypothesis in the lab is that there will be a correlation between our genes of interest, i.e., mutations in both genes would occur together to promote tumorigenesis and a more aggressive phenotype.
We have reached a frustrating halt. I really want to get through this. We basically want to extract mutation data for two genes in the same cohort. I'm trying to work with Firebrowse and FirebrowseR, which seem like the most promising tools for this, but to no avail. Could someone point me in the right direction? Any advice will be very appreciated. Thank you!