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


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Documentation for package ‘mdp’ version 1.24.0

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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