This repository provides R scripts on the analysis of the following publication:
The analysis contains following steps: A) Processing of CPTAC iTRAQ DDA data downloaded from CPTAC data portal to a complete and filtered protein matrix. SCRIPT: 1_iTRAQ_protein_processing.R INPUT: Downloaded protein level data from CPTAC data portal analyzed with Common Data Analysis Pipeline (CDAP) OUTPUT: CPTAC_DDA_protein_level_CDAP.Rdata containing DDA and DDA_missing0
B) Processing the output from the described OpenSWATH, pyProphet, TRIC pipeline with SWATH2stats and mapDIA for protein inference SCRIPT: 2_SWATH_preprocessing.R 3_SWATH_norm_batch.R 4_mapDIA_parameter INPUT: feature_alignment.tsv can be downloaded from ProteomeXchange OUTPUT: fragments_for_protein_quantification.txt
C) Processing the mapDIA output of SWATH data to a final filtered and imputed protein matrix SCRIPT: 5_SWATH_processing.R INPUT: fragments_for_protein_quantification.txt OUTPUT: CPTAC_SWATH_peptide_level.Rdata contains several intermediate steps, data_peptide, data_pepratio, data_pepratio_log CPTAC_SWATH_protein_level.Rdata contains the full unfiltered SWATH protein data data_protein CPTAC_SWATH_protein_level_filtered.Rdata contains the SWATH data after filtering (with gene names) SWATH_filtered CPTAC_SWATH_imputed.Rdata contains SWATH data with imputed values SWATH_imputed Figure S1C
D) Analyze SWATH data and iTRAQ data for technical details like peptide and protein variability, completeness and correlation SCRIPT: 6a_CPTAC_completeness.R 6b_CPTAC_correlation.R 6c_CPTAC_peptide_variability.R INPUT: CPTAC_SWATH_protein_level.Rdata (data_protein) CPTAC_DDA_protein_level_CDAP.Rdata (DDA, DDA_missing0) CPTAC_SWATH_imputed.Rdata (SWATH_imputed) CPTAC_SWATH_peptide_level.Rdata (data_pepratio) PSM files from CPTAC data portal OUTPUT: Figure S1A and B Figure 2A-C CPTAC_SWATH_overlap.Rdata contains matrix with common proteins SWATH_overlap CPTAC_DDA_overlap.Rdata contains matrix with common proteins DDA_overlap SWATH_iTRAQ_correlations.Rdata
E) Comparison of molecular subtype classification SCRIPT: 7a_CPTAC_Classification.R 7b_CPTAC_WGCNA.R 7c_CPTAC_heatmap.R INPUT: CPTAC_SWATH_overlap.Rdata CPTAC_DDA_overlap.Rdata CPTAC_DDA_protein_level_CDAP.Rdata (DDA_missing0) CPTAC_SWATH_protein_level.Rdata (data_protein) classification_result_template.csv clinical_data.csv OUTPUT: SWATH_classification_workflow.Rdata DDA_classification_workflow.Rdata classification_result.Rdata Figure 3 Figure S2A
F) Bootstrapping algorithm for classification stability and mesenchymal stability SCRIPT: 7d_CPTAC_stability.R INPUT: classification_result.Rdata CPTAC_DDA_protein_level_CDAP.Rdata CPTAC_SWATH_imputed.Rdata SWATH_classification_workflow.Rdata DDA_classification_workflow.Rdata OUTPUT: Figure 4A-D Figure S2B
G) Differential expression analysis of previously identified molecular subgroups SCRIPT: 7e_CPTAC_class_comparison.R INPUT: CPTAC_DDA_WGCNA.Rdata CPTAC_SWATH_WGCNA.Rdata SWATH_iTRAQ_correlations.Rdata CPTAC_SWATH_imputed.Rdata CPTAC_DDA_protein_level_CDAP.Rdata OUTPUT: Figure 5 Figure 6
H) Analysis of HRD vs. non-HRD subgroups SCRIPT: 8a_mapDIA_HRD_input 8b_HRD_Volcano.R 8c_HRD_network_smoothing.R INPUT: mapDIA_input_norm_batchcorr.tsv OUTPUT: Figure 7