RNA Harmonization Analysis App

Welcome to the RNA Harmonization Study Analysis repository!

Links

• The live dashboard is available !TODO.
• The paper for this study is available !TODO.

Organization

• All data files from the study are under /data

  • 20210603 MassCPR.csv -- data from the tech dev platform at MassCPR
  • 20210603 NIST-NML-NIB.csv -- data from National Labs, different experiment design
  • 20210810_normal_labs.csv -- data from other labs, formatted consistently
  • 20230223 PoC.csv -- Proof of Concept experiment data

• Source code is in /R, which is organized into folders according to purpose.

• The app is composed from a shiny server and ui, specified in app_server.R and app_ui.R respectively.

• Calibration functions are specified in calibration_utils.R:

  • calAndPredict()
  • fitCal()
  • fitGroup()
  • calcResults()

• Data i/o functions are specified in data_intake.R

  • getPoC(): reads in the Proof of Concept data from a .csv.
  • getStudyData(): combines data read in from the rest of the .csvs associated with the study.

• Functions which plot visualizations from the study data are specified in plotting_utils.R

  • plotCal()
  • sampleByRank()
  • sampleByLabTarg()
  • comparePlot()

• Functions which create tables from the study data are specified in table_utils.R

  • materialTable()
  • materialSummary()
  • labTargTable()

• Functions which process the Proof of Concept data reside in poc_utils.R

  • plot_poc_results()
  • calibPoC()

• And finally, functions to create and save publication-ready plots are in makePubPlots.R

  • pubBoxPlots1b()
  • pubResults2a()
  • pubPoC2b()