Commenting, Changelog, and initial phenotype inclusion #195
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Short description for each function in tinypeel and PeelingIO
- Update to user manual - Two new input files: phenotype and phenotype penetrance - New output parameter to print out pheno_prob - update penetrance for phenotype. At the moment this is for one phenotype and single locus. - function to calculate the phenotype probabilities from inputted penetrance and genotype probabilities. - function to write out the pheno type probabilities
Removal of comments and handling of errors.
-Functional tests for phenotype file input and phenotype penetrance.
Commenting in docString format on all functions in AlphaPeel module (not submodules, i.e tinyhouse)
Additional text to clarify the approach for phenotype data input and phenotype penetrance under the current functionality (one phenotype to one genotype).
- Commenting on all functions - New changelog - Functionality for inclusion of a single phenotype and associated testing.
…aPeel into feat_pheno_info
XingerTang
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Oct 15, 2025
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XingerTang
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XingerTang
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Hi @RosCraddock, I left some comments.
Thank you for all the documentation work, it would help a lot for the later development.
7 tasks
- temporary user warning where multiple phenotypes are provided.
testcase "multi_pheno_state" added.
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This is quite a large pull request combining two aspects:
Welcome any feedback and/or questions!