Chris' suggestions

[caalo]

• Formatted code, removed unused variables
• Should be able to run the entire analysis via TCGA_analysis Updated June2026.R!
• Added imports to load in all the functions! ie, source("TCGA_analysis Function 2026.R")
• In the previous version, variables such as clinical, expression, and data_se that were originally defined in the main code (TCGA_analysis Updated June2026.R) are used in the functions. This is generally not best coding practice as it make the functions not modular (and in other coding languages, these variables are at the risk of being modified within the function), as the function depends on having these variables defined in the first place. What is usually done is that these variables are passed into the function as inputs also, to make the function self-contained. I have modified the functions to take in two new variables summarized_experiment and normalized_expression, and clinical and row_info are derived from summarized_experiment within the function. So when we call the function, we have to give these new inputs as well!
• Composite analysis is now a function compositeSurvivalAnalysis(). Even though we are not iterating through genes, it's nice to be able to call the code with a function so you don't have to manually run it.