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pyPheWAS

Repository for the pyPheWAS project. Full documentation at https://pyphewas.readthedocs.io/en/latest/

Developers

Cailey Kerley, PhD

Shikha Chaganti, PhD

Bennett Landman, PhD

Cite pyPheWAS

Kerley, C.I., Chaganti, S., Nguyen, T.Q. et al. pyPheWAS: A Phenome-Disease Association Tool for Electronic Medical Record Analysis. Neuroinform (2022). https://doi.org/10.1007/s12021-021-09553-4

Kerley, C.I., Nguyen T.Q., Ramadass, K, et al. pyPheWAS Explorer: a visualization tool for exploratory analysis of phenome-disease associations. JAMIA Open (2023). https://doi.org/10.1093/jamiaopen/ooad018

Latest Release: pyPheWAS 4.2

4.2.0

  • Default regression equation modified to allow for both canonical and reversed PheWAS equations
  • Updated plot styling to improve legibility
  • Bug fix: can now run pyPhewasModel/pyProwasModel without covariates
  • Other minor bug fixes

4.1.1

  • Minor bug fixes

4.1.0

  • pyPheWAS Explorer updates
  • New demographic variables added to synthetic dataset

4.0.5

  • convertEventToAge includes new warning for calculated ages are negative
  • small bugs fixed in maximizeControls, NoveltyAnalysis, and PubMedQuery tools

4.0.4

  • createPhenotypeFile now supports more options for controlling case/control group curation
  • Documentation updates

4.0.3

  • Novelty Analysis tools: examine the relative literary novelty of disease-phecode pairings
  • pyPheWAS Explorer: an interactive visualization of PheDAS experiments
  • createGenotypeFile updated - now called createPhenotypeFile
  • Minor bug fixes

Older Releases

pyPheWAS 3.2.0

  • Configurable threshold for number of subjects required to run the regression on an individual PheCode
  • All regressions are now fit with regularization (old scheme available with 'legacy' option)
  • Minor changes to Manhattan plot
  • PheCode/ProCode categories added to regression file
  • Minor bug fixes

pyPheWAS 3.1.1

  • New Analysis Type: ProWAS Tools
  • New Plot Type: Volcano Plot (see pyPhewasPlot)
  • maximizeControls now saves explicit Case/Control matches
  • New PheCode category colors in plots are more distinguishable
  • Improved command line tool argument handling
  • Improved error handling
  • Documentation overhaul
  • API update
  • Minor bug fixes

pyPheWAS 3.0.1

  • Bug fixes including FDR & Bonferroni threshold calculations
  • Header saved in feature matrices
  • More file formats available for saving plots

pyPheWAS 3.0.0

  • Support for both ICD 9 and ICD 10
  • All 3 regression types (binary, count, & duration) optimized for big data
  • pyPhewasPipeline: a streamlined combination of pyPhewasLookup, pyPhewasModel, and pyPhewasPlot
  • Compatibility with Python 3
  • Age matching now saves the explicit mapping between controls/cases in addition to the resulting group file
  • Operation of the ICD censoring function matches the description in the documentation
  • Minor bug fixes