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Add batch_correct_counts() #87

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Add batch_correct_counts() #87

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@kelly-sovacool kelly-sovacool commented Jan 30, 2025

Changes

Add batch_correct_counts() based on NIDAP template. Uses sva::ComBat() for batch correction.

Issues

resolves #19

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • Write unit tests for any new features, bug fixes, or other code changes.
  • Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
  • Update NEWS.md with a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.html
  • Run devtools::check() locally and fix all notes, warnings, and errors.

@kopardev kopardev added the MOSuite RepoName label Jan 30, 2025
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codecov bot commented Jan 30, 2025

Codecov Report

Attention: Patch coverage is 69.82249% with 51 lines in your changes missing coverage. Please review.

Project coverage is 74.03%. Comparing base (5f642e3) to head (fc74e5e).

Files with missing lines Patch % Lines
R/batch-correction.R 68.65% 21 Missing ⚠️
R/clean.R 59.09% 18 Missing ⚠️
R/utils.R 45.45% 6 Missing ⚠️
R/filter.R 80.00% 4 Missing ⚠️
R/histogram.R 50.00% 1 Missing ⚠️
R/normalize.R 92.30% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #87      +/-   ##
==========================================
- Coverage   75.08%   74.03%   -1.05%     
==========================================
  Files          14       15       +1     
  Lines         590      674      +84     
==========================================
+ Hits          443      499      +56     
- Misses        147      175      +28     

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batch effect correction
3 participants