Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix bedgraph error due to NA handling in meth.diff export #332

Draft
wants to merge 2 commits into
base: master
Choose a base branch
from
Draft

Fix bedgraph error due to NA handling in meth.diff export #332

wants to merge 2 commits into from

Commits on Nov 12, 2024

  1. Fix bedgraph error due to NA handling in meth.diff export 

    Fixes #331

Fix the error in `tests/testthat/test-17-bedgraph.r` due to NA handling in `meth.diff` export as log-transformed value.

* **R/bedgraph.R**
  - Disallow transformation of `meth.diff` values in `bedgraph` function for `methylDiff` objects.
  - Add a check to ensure `log.transform` is `FALSE` when `col.name` is `meth.diff`.

* **tests/testthat/test-17-bedgraph.r**
  - Update tests to ensure `log.transform` is not allowed for `meth.diff` values.
  - Add a test to check for error when `log.transform` is `TRUE` for `meth.diff`.
  - Add tests for `methylDiffDB` objects to ensure `log.transform` is not allowed for `meth.diff` values.

* **R/methylDBFunctions.R**
  - Add a check to ensure `log.transform` is `FALSE` when `col.name` is `meth.diff`.
  - Disallow transformation of `meth.diff` values in `bedgraph` function for `methylDiffDB` objects.

---

For more details, open the [Copilot Workspace session](https://copilot-workspace.githubnext.com/al2na/methylKit/issues/331?shareId=XXXX-XXXX-XXXX-XXXX).
    @alexg9010
    alexg9010 committed Nov 12, 2024
    Configuration menu
    Copy the full SHA
    82f3081 View commit details
    Browse the repository at this point in the history

  2. Update test-17-bedgraph.r 

    compare length with number of stored records
    @alexg9010
    alexg9010 authored Nov 12, 2024
    Configuration menu
    Copy the full SHA
    f9a2ae4 View commit details
    Browse the repository at this point in the history