R scripts and input files for the manuscript "Higher-order modular regulation of the human proteome".
R scripts are in main folder, all files that are read into R scripts are in input_files folder, all files that are created by an R script are in the output_files folder.
Half-life-analysis.R Script that creates Extended Data Figure 3, analysing mRNA and protein half-lives of progulons
WGCNA_proteomeHD_treeClust.R Script that clusters the ProteomeHD + treeClust distance matrix hierachical via WGCNA package
core_modules_clustering.R Script that creates the seeds by overlapping OPTICS and ClusterONE (external Java application) clustering
prn_checkup.R Does some basic filtering, e.g. removing all progulons that have an AUC > 0.99.
prn_connectivity Calculates a connectivity score for each progulon at random forest score cut-offs from 0.5 to 1.0 in 0.01 increments, removing one progulon that is not a significantly connected module at any cut-off
prns_correlation.R Calculates and plots the Spearman's correlation between non-overlapping proteins of progulons
prns_overlap.R Calculates and plots the overlap in numbers and percentage between the progulons
prns_basic_stats.R Calculates and plots some basic statistics about each progulon (how many proteins etc)
prns_examples_tSNE.R Produces plots showing three example progulons
prns_functional_enrichment.R plots numbers of significant enrichments of GO terms (topGO), Reactome pathways and humap2 complexes in progulons