Create plots comparing how different consensus thresholds affect gene set sizes and p-values in GATAI analysis.
threshold_comparison_plots(phyex_set, runs)A list with two ggplot objects:
Plot showing gene counts across thresholds
Plot showing p-values across thresholds
A PhyloExpressionSet object
List of GATAI run results
This function analyzes how the choice of consensus threshold (minimum number of runs a gene must appear in) affects the final gene set size and statistical significance. Uses cached null distributions for efficient p-value calculation. # Create threshold comparison plots # thresh_plots <- threshold_comparison_plots(phyex_set, gatai_runs)