Goal
Provide a warning or an error to the user when a phenotype penetrance probability file is used incorrectly. For example, where the rows of the phenotype penetrance probability file do not sum to 1.
Proposed approach
When reading in the phenotype penetrance probability file, check that the rows sum to 1 (or very nearly). If they do not, produce an error to the user identifying the row. Instruct the user to correct or not include phenotypes.
Scope
The submodules (tinyhouse) pedigree.py file only.
Done when
Once change has been completed in tinyhouse and the submodule updated in AlphaPeel
Note that these changes will occur in tinyhouse only (submodule), but creating an issue here to ensure the submodule is updated once complete.
Goal
Provide a warning or an error to the user when a phenotype penetrance probability file is used incorrectly. For example, where the rows of the phenotype penetrance probability file do not sum to 1.
Proposed approach
When reading in the phenotype penetrance probability file, check that the rows sum to 1 (or very nearly). If they do not, produce an error to the user identifying the row. Instruct the user to correct or not include phenotypes.
Scope
The submodules (tinyhouse) pedigree.py file only.
Done when
Once change has been completed in tinyhouse and the submodule updated in AlphaPeel
Note that these changes will occur in tinyhouse only (submodule), but creating an issue here to ensure the submodule is updated once complete.