## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----------------------------------------------------------------------------- library(mdp) data(example_data) # expression data has gene names in the rows data(example_pheno) # pheno data needs a Sample and Class column mdp.results <- mdp(data=example_data, pdata=example_pheno, control_lab = "baseline") ## ----------------------------------------------------------------------------- sample_scores_list <- mdp.results$sample_scores # select sample scores calculated using the perturbed genes sample_scores <- sample_scores_list[["perturbedgenes"]] head(sample_scores) sample_plot(sample_scores,control_lab = "baseline", title="perturbed") ## ----------------------------------------------------------------------------- zscore <- mdp.results$zscore ## ----------------------------------------------------------------------------- gene_scores <- mdp.results$gene_scores gene_freq <- mdp.results$gene_freq head(gene_scores) ## ----------------------------------------------------------------------------- perturbed_genes <- mdp.results$perturbed_genes ## ----results='hide',fig.show = 'hide'----------------------------------------- file_address <- system.file("extdata", "ReactomePathways.gmt", package = "mdp") pathways <- fgsea::gmtPathways(file_address) mdp.results <- mdp(data=example_data, pdata=example_pheno, control_lab = "baseline",pathways=pathways) ## ----------------------------------------------------------------------------- head(mdp.results$pathways) sample_scores <- mdp.results$sample_scores[["Interferon alpha/beta signaling"]] sample_plot(sample_scores,control_lab = "baseline", title="Interferon a/b") ## ----results='hide',fig.show = 'hide'----------------------------------------- mdp.results <- mdp(data=example_data, pdata=example_pheno, control_lab = "baseline", measure = "mean") ## ----------------------------------------------------------------------------- control_samples <- example_pheno[example_pheno$Class == "baseline","Sample"] zscore <- compute_zscore(data = example_data,control_samples = control_samples,measure = "mean",std = 2)