Custom copy number tumor cohort normalization for isolating effects of individual CNAs
First, call the ChrArm_CNA_freq_TCGA_puritycorrection.r function to generate purity-corrected copy number calls and CNA summaries.
Then use the output to call Arm_Level_CNorm_diffexp.r function to analyze differential expression associated with a CNA.
This function will perform cohort subsampling to normalize co-occuring CNAs when possible. To simply generate differential expression data without cohort subsampling and CNA normalization, set cohort_subsample_minFrac = 0.
