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 |