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Contribute: Adding a New Method to methyldeconv

Source: vignettes/contribute.Rmd
contribute.Rmd

Contributing a New Method to methyldeconv

Thank you for your interest in contributing to methyldeconv! This guide will help you add a new cell-type deconvolution method to the package.

1. Fork and Clone the Repository

2. Add Your Method Implementation

  • Add a new R script for your method in the R/ directory (e.g., mynewmethod.R).
  • Follow the structure of existing methods (see files like epidish.R, houseman.R, etc.).
  • Your function should:
    • Accept a beta matrix or methylSet as input.
    • Return results in a format consistent with other methods (see run_epidish, run_houseman, etc.).
    • Include roxygen2 documentation.

3. Register Your Method

  • If your method should be accessible via the unified interface (deconvolute or deconvolute_combined), update the relevant logic in main.R.
  • Add your method to the list of supported methods and document any new parameters.

4. Expose All Method Parameters via methyldeconv

To ensure users can fully utilize your new method, make sure that all relevant parameters of your function are accessible through the main methyldeconv interfaces (deconvolute and/or deconvolute_combined).

  • Update the argument handling in main.R so that users can pass any method-specific parameters when calling these functions.
  • Clearly document these parameters in your function’s roxygen2 documentation and in the main interface documentation if needed.
  • This approach ensures flexibility and makes your method as useful as possible for a wide range of use cases.

5. Document Your Method

  • Add a roxygen2 documentation block to your function.
  • Run devtools::document() to update the manual files in man/.
  • Optionally, add an example to the README or a new vignette.

6. Add Tests

  • Add tests for your method in tests/testthat/ (see test_methods.R for examples).
  • Ensure your method is covered by the test suite.

7. Check and Build

  • Run devtools::check() to ensure your changes pass all checks.
  • Build the documentation site locally with pkgdown::build_site() to preview your changes.

8. Submit a Pull Request

  • Push your branch to your fork and open a pull request against the main repository.
  • Describe your changes and reference any related issues.

9. Code Review

  • Address any feedback or requested changes from the maintainers.

For more details, see the pkgdown documentation and the R packages book.

If you have questions, feel free to open an issue or ask for help in your pull request!