runModac

To-Do

• 1. Have unified input file with separate sheets for each method and only sample names, no group names needed here
• 2. Plot ISTDs
• 3. Normalize each method by ISTD or IQR
• 4. Merge methods to make a combined normalized dataset
• 5. Plot QCs
• 6. Drop QCs from normalized dataset
• 7. Save excel file with normalized data
• 8. Extract comparisons and settings from a separate excel file with a separate sheet for the settings and then separate sheets for each comparison containing
  • a. Comparison – A_over_B
  • b. Statistical test – t-test or ANOVA
  • c. Group order – B, A
  • d. Group and sample names
    • i. This helps define new groups when there are overlapping groups in comparisons
• 9. Perform statistical tests for each comparison and save
  • a. t-test reports with
    • i. LogFoldChange
    • ii. LinearFoldChange
    • iii. p-value
    • iv. FDR
  • b. ANOVA reports with
    • i. p-value
    • ii. FDR
  • c. Boxplots of each feature for each comparison
  • d. Heatmaps for each comparison of
    • i. All features
    • ii. Only significant features passing FDR threshold
  • e. Excel files containing underlying data used to generate heatmaps
• 10. Generate pptx report summarizing results, similar to python pipeline