R/examples/markers_distribution_example.R

In combiroc: Selection and Ranking of Omics Biomarkers Combinations Made Easy

\dontrun{
demo_data # combiroc built-in demo data (proteomics data from Zingaretti et al. 2012 - PMC3518104)

demo_data_long <- combiroc_long(data = demo_data) # long format data




# To visualize the distribution of the expression of each marker.

distributions <- markers_distribution(data_long = demo_data_long,
                                       boxplot_lim = 1500, y_lim = 0.001,
                                       x_lim = 3000 , signalthr_prediction = FALSE,
                                       case_class = 'A', min_SE = 40, min_SP = 80)

distributions$Density_plot # density plot
distributions$Density_summary # summary statistics of density plot
distributions$ROC # ROC showing signal threshold range ensuring min SE and/or SP
distributions$Coord # ROC values
distributions$Boxplot # Boxplot
}