I am looking to compare mutation frequencies between two databases, for example TCGA and cbioportal for the same set of genes.
I understand that Fishers exact maybe the most suitable format. But, I am not able to wrap my head around the actual input data needed for this.
Sample information I have:
Gene cbioportal_n cbioportal_mutation_Freq_per_model TCGA_n TCGA_mutation_Freq Gene1 91 76.0% 128 72.7%
Also, If there is a way to automate this process in a script with R/ python options.