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Draft of vignette for rare variant scoring
…coring into penetrance_vignette
bballew
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May 6, 2025
R/pedigree.r
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K is the penetrance value, as estimated by the optimization function. I used K because the paper I was referencing used K; it's also often used to set seeds to I can see the confusion!
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Okay I see, I think I understood it (the optimization is trying K values between c(0,1) and returning the output best K). I was not sure how to best describe this input range. I will rework the param definition.
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would a default argument of c(0,1) make sense here?
…coring into penetrance_vignette
Adding in new unit tests for pedigree scoring, bug fix for multiple-tree acutal `d` and `n` values. Fixes some essential bugs.
Adding error handling for variant encodings
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Readme expanded to improve user experience
Green checkmark, wooo. Note I won't add the status badge to the README in anticipation of some day putting this on CRAN. From my experience that and any images in the README need to get stripped out, so its easiest to keep things barebones and not have to maintain multiple styles of the readme on different branches..
Rename to KinformR, all internal references changed. Package still passes unit tests, build, and documentation tests. Now updated the GitHub web page as well.
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Hi @bballew,
I've taken an initial go at refactoring the methods from seqbio-pedigree-ranking into a module for this R package.
Your review is appreciated, as I think I have grasped the meaning of all the params and the parts of the process, but I would like a second opinion on whether the documentation of the functions is a good reflection of everything that is going on. Please correct any mistakes I've made.
In terms of next steps we can:
Also I think a means of encoding the input matrix from a standard format would be a nice to have, but not required right now.
Addresses #12