Support UniFrac and pre-calculated dissimilarity in getPERMANOVA (#844) - #846
Merged
Merged
Conversation
- Add dis.name to getPERMANOVA,SummarizedExperiment to retrieve pre-calculated dissimilarity matrices from metadata(x).
- Automatically delegate to mia::getDissimilarity() when method %in% c('unifrac', 'overlap', 'jsd').
- Allow getPERMANOVA,ANY to accept dist objects directly and align sample metadata rows by sample names.
- Update .calculate_homogeneity() in runCCA.R to accept dist and symmetric matrices without re-running vegdist().
- Add unit tests covering on-the-fly UniFrac, direct dist inputs, dis.name usage, and input validations.
- Synchronize documentation and examples in man/getPERMANOVA.Rd.
…o 844-permanova-unifrac
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #846 +/- ##
==========================================
+ Coverage 74.71% 74.81% +0.09%
==========================================
Files 62 62
Lines 7530 7543 +13
==========================================
+ Hits 5626 5643 +17
+ Misses 1904 1900 -4 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
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
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Resolves #844. Extends
getPERMANOVAandaddPERMANOVAto support UniFrac and pre-calculated dissimilarity matrices. Tree-aware metrics (unifrac,overlap,jsd) are computed viamia::getDissimilarity(), and pre-calculated matrices can be retrieved viadis.namefrommetadata(x)or passed directly asdistobjects. Also updates dispersion testing in.calculate_homogeneity()to accept distance objects directly.