# Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

## Documentation for package ‘mdp’ version 1.31.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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