5 Simulation Evaluation

This chapter introduces the simulation utilities in normpatch. The two main functions are sim_gene_counts() and def_DEG(). sim_gene_counts() generates artificial RNA-seq count matrices, and def_DEG() defines the true DEG status from the simulation parameters and a fold change threshold. These functions are useful for checking normalization behavior under controlled settings, especially when DEGs are intentionally biased toward one group.

The examples in this chapter are intended as practical templates. For a formal benchmark, repeat each simulation many times, vary the simulation parameters, and summarize performance across simulation replicates rather than relying on one dataset.