This is a very simple app for calculating and displaying the approximately ascertainment-corrected penetrance estimate (hereafter f-tilde) and the corresponding uncorrected penetrance estimate (hereafter f-tilde-star) given variables alpha, f, s, and k, and showing distributions of those calculations as a function of a number of simulated families. In essence, this serves as a pair of "interactive figures".
For details on what is going on here, please see the paper this app is intended to accompany:
Paterson AD, Seok S-C, Vieland VJ. The effect of ascertainment on penetrance estimates for rare variants: implications for establishing pathogenicity and for genetic counseling. PloS ONE, 2023; doi:10.1371/journal.pone.0290336
- Python 3.7 or higher
- PyQt5
- seaborn (and thus matplotlib)
- pandas
- Start the program by running
python3 PenEstApp. - Enter in values for presented variables as desired.
- Press the "Refresh Plot" button.
Summary statistics may be saved to a plain text file using the "Save statistics to file" button. There is also a "Save plot image to file" button; image format will default to PNG, but you can specify a different image file format by typing in that format's file extension at the end of the filename. Finally, "Save raw output" saves a CSV file of all plotted data.
- As s increases (particularly as it goes above 5), refreshes slow down considerably because of the calculation time required. We intend to add a warning dialog to indicate this.
- The default (on launch) number of sim replicates for Figure 1 is set at 100. On older computers this may take a while to finish (minutes or more).
Matthew Parker for the "sinaplot" code.