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+# .R code for GC Metabolomics and LC-MS/MS Proteomics
+
+### GC_metabolomics_heatmap.R
+
+**description**:   
+    1. Load data from SQLlite data base (Metabolomics normalized measurements, deidentified patient meta data, and metabolite class meta)  
+    2. Data formatting from long to wide format  
+    3. Meta formattting to pad all single digit patient id's with a zero  
+    4. Generate heatmap with annotations (177 metabolites) for Controls, NONCOVID, and COVID patients  
+    5. Remove Controls  
+    6. Exploratory figures for COVID and NONCOVID metabolomics  
+    7. Fold Changes to median NONCOVID  
+    8. Filter features witth fold changer greater than 4.2 in at least one patient  
+    
+**Relevant Issue(s)**: Unsupervised analysis #3  
+**date created**: 5/26/20  
+**date last modified**: 5/26/20  
+**input**:  
+  - sqlite_db: data/SQLite Database/Covid-19 Study DB.sqlite  
+
+**output**:  
+  - NA  
+ 
+### Proteomics_heatmap.R
+
+**description**:   
+    1. Load data from SQLlite data base (Proteomics normalized measurements, deidentified patient meta data, and proteomics meta)  
+    2. Data formatting from long to wide format  
+    3. Meta formattting to pad all single digit patient id's with a zero  
+    4. Fix raw file names for HC and pooled plasma.
+    5. Generate heatmap with annotations (517 proteins) for Human Controls (HC), pooled plasma, NONCOVID, and COVID patients  
+    6. Remove HC and pooled plasma samples  
+    7. Exploratory figures for COVID and NONCOVID proteomics  
+    8. Fold Changes to median NONCOVID  
+    9. Fold Changes to median NONCOVID not in the ICU 
+    
+**Relevant Issue(s)**: Unsupervised analysis #3  
+**date created**: 5/27/20  
+**date last modified**: 5/27/20  
+**input**:  
+  - sqlite_db: data/SQLite Database/Covid-19 Study DB.sqlite  
+
+**output**:  
+  - NA 
+
+### Protein_peptide_90minSingleShot_COVID_CoagulationCascade.R 
+
+description: Generates csv's for each protein in MaxQuant proteingroups.csv, where each csv contains the  peptide measured in MS/MS analysis for that specific protein.
+Relevant Issue(s): NA
+date created: 5/26/20
+date last modified: 5/26/20  
+**input**:  
+  - protein groups csv: P:/All_20200428_COVID_plasma_multiomics/Proteomics/90 min single-shot reps for Anji/combined_includingIsoforms_Deane_coagulationPathway/txt/peptides_Plasma_90SingleShot.csv  
+  - peptides csv: P:/All_20200428_COVID_plasma_multiomics/Proteomics/90 min single-shot reps for Anji/combined_includingIsoforms_Deane_coagulationPathway/txt/peptides_Plasma_90SingleShot.csv
+  - Uniprot gene csv: P:/All_20200428_COVID_plasma_multiomics/Proteomics/90 min single-shot reps for Anji/UniprotDatabase_CoagulationCascade_List.csv  
+
+**output**:  
+  - peptide csv for each gene: All_20200428_COVID_plasma_multiomics/Proteomics/90 min single-shot reps for Anji/CoagulationCascade_peptide_data/