search

bystrogenomics / bystro

High Dimensional Machine Learning Toolkit with applications in Genetics & Proteomics
Apache License 2.0
43 stars 16 forks source link

Parent of Origin Verify Data Match Model Assumptions #584

Open austinTalbot7241993 opened 3 days ago

austinTalbot7241993 commented 3 days ago

We can save massive amounts of computational effort verifying that the data match the model assumptions, namely that the variance observed in the heterozygotes should match or exceed the homozygotes. If this fails we might as well save the computation time and artificially force non-significance of the SNP.

Summary by CodeRabbit

coderabbitai[bot] commented 3 days ago

Walkthrough

The changes introduce a new parameter, assess_model_assumptions, to the constructors of two classes in the parent_of_origin.py file. This parameter, which defaults to True, controls whether the model checks for violations of assumptions regarding variances between homozygotes and heterozygotes during the fitting process. If violations are detected, the method will return early, setting specific output values accordingly. Additionally, modifications in the test file enhance the data generation process.

Changes

Files Change Summary
python/python/bystro/parent_of_origin/parent_of_origin.py Added assess_model_assumptions: bool = True to the constructors of two classes. Updated the fit method to include checks based on this parameter.
python/python/bystro/parent_of_origin/tests/test_parent_of_origin.py Increased the number of individuals in data generation from 20,000 to 200,000 and introduced new variables X and y for phenotypes and genotypes.

Possibly related PRs

Poem

In the land of code where rabbits hop,
A new parameter helps us stop!
With checks for variances, oh so bright,
We ensure our models fit just right.
Hooray for changes, let’s give a cheer,
For assumptions kept safe, we have no fear! 🐇✨

📜 Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
📥 Commits Files that changed from the base of the PR and between 115720b4573a789877bc6539c6e0043b2bf03516 and 8c201103d97b0e81fde08743191b4e394e3b62bb.
📒 Files selected for processing (1) * python/python/bystro/parent_of_origin/parent_of_origin.py (7 hunks)
🚧 Files skipped from review as they are similar to previous changes (1) * python/python/bystro/parent_of_origin/parent_of_origin.py
--- Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?
❤️ Share - [X](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)
🪧 Tips ### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit , please review it.` - `Generate unit testing code for this file.` - `Open a follow-up GitHub issue for this discussion.` - Files and specific lines of code (under the "Files changed" tab): Tag `@coderabbitai` in a new review comment at the desired location with your query. Examples: - `@coderabbitai generate unit testing code for this file.` - `@coderabbitai modularize this function.` - PR comments: Tag `@coderabbitai` in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples: - `@coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.` - `@coderabbitai read src/utils.ts and generate unit testing code.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` - `@coderabbitai help me debug CodeRabbit configuration file.` Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. ### CodeRabbit Commands (Invoked using PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger an incremental review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai full review` to do a full review from scratch and review all the files again. - `@coderabbitai summary` to regenerate the summary of the PR. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai configuration` to show the current CodeRabbit configuration for the repository. - `@coderabbitai help` to get help. ### Other keywords and placeholders - Add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. - Add `@coderabbitai summary` to generate the high-level summary at a specific location in the PR description. - Add `@coderabbitai` anywhere in the PR title to generate the title automatically. ### CodeRabbit Configuration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - Please see the [configuration documentation](https://docs.coderabbit.ai/guides/configure-coderabbit) for more information. - If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: `# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json` ### Documentation and Community - Visit our [Documentation](https://coderabbit.ai/docs) for detailed information on how to use CodeRabbit. - Join our [Discord Community](https://discord.com/invite/GsXnASn26c) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.