Accommodate changes from DropletUtils::emptyDrops()#20
Merged
PeteHaitch merged 5 commits intodevelfrom Apr 3, 2025
Merged
Conversation
- Details of changes: MarioniLab/DropletUtils#118 - Since the default is now `alpha=Inf`, the claims around `alpha` values and sanity check no longer make sense, so just remove them.
- Details of changes: MarioniLab/DropletUtils#118 - For this chunk, the new default of `alpha=Inf` gives poor results. Some quick comparisons given below - BioC 3.21 - 39,028 non-empty droplets with `emptyDrops(counts(hto.sce), by.rank=40000)` - 21,374 non-empty droplets with `emptyDrops(counts(hto.sce), by.rank=40000, alpha=NULL) - 29,673 non-empty droplets with `emptyDrops(counts(hto.sce), by.rank=30000)` - BioC 3.20 - 21780 on-empty droplets with `emptyDrops(counts(hto.sce), by.rank=40000) (i.e. former default of `alpha = NULL`) - Added some explanation/justification cribbed from that removed in 76a88c5
- Not directly related to emptyDrops changes, but perhaps indirectly?
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
These changes ensure the book now builds for me locally on my Ubuntu machine.
Will push to BioC's git to have the Bioconductor build system try it out.