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 1.29.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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