Repository navigation
Sync numeric Limma group-label support - #3
Merged
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Outcome
Synchronizes canonical OMIX Limma Analysis
0.1.1into the Code Ocean adapter and adds adapter-level regression coverage for numeric modeled-group labels and contrast1-0.Closes #2.
Files changed
code/functions/OMIX_Limma_Analysis.R: byte-identical export from canonical OMIX commitdb70975167807d10634d5af33fc49828e32be633.OMIX_MODULE_SOURCE.mdandtests/test-source-parity.py: updated canonical version, immutable reference, and SHA-256446d1eab1f9f10d28f1b5f7f35281c6c694d206ddd5554b0ccdb6a377a87f30a.tests/test-pseudobulk-handoff.R: numeric0/1group and1-0contrast regression.README.mdandCHANGELOG.md: user-facing compatibility note and pending adapter change.Scientific behavior
Scientific code flows only from canonical OMIX to this adapter. No Code Ocean discovery, parameter translation, runtime, output location, or default changed.
Validation
git diff --checkbash tests/run-tests.shmodules/OMIX-Limma-Analysis/R/OMIX_Limma_Analysis.RAll local adapter checks passed.
External validation remaining
After merge and Code Ocean sync, rerun capsule
8635652with the exact Harmony bundle from Pseudobulk run1207597,contrast_variable_columns = Group,contrasts = 1-0, andvariance_model = auto. Confirm successful outputs andauto -> ebayes.No adapter tag or Code Ocean release is authorized by this PR.