There are a number of scripts involved in this stage.
expressionSummarizer.r
prepares expression data columns and Id valuesgeneIdConverter.r
uses a Bioconductor annotation package to unify gene symbolsprepare_mutation.py
prepares mutation data by removing useless columns and unwanted rows.preprocessing.py
this code generates a summary for each cancer that will be further used to aggregate in the next stageby running each python script with a --help
flag you will learn more about input args.