compute_gene_score      Compute gene score Computes gene scores for
                        each gene within each class and perturbation
                        freq
compute_perturbed_genes
                        Compute perturbed genes Find the top fraction
                        of genes that are more perturbed in test versus
                        controls
compute_sample_scores   Compute sample scores for each pathway
compute_zscore          Computes the thresholded Z score Plots the Z
                        score using control samples to compute the
                        average and standard deviation
example_data            Expression data example
example_pheno           Phenotypic data example
mdp                     Molecular Degree of Perturbation
pathway_summary         print pathways generates a summary plot for
                        pathways and sample score plot of best gene set
sample_data             Sample score results
sample_plot             Plot sample scores Plots the sample scores
                        data.frame for a given geneset.  Data frame
                        must have Score, Sample and Class columns
