Add atac_marker_peaks component#879
Open
VladimirShitov wants to merge 17 commits into
Open
Conversation
DriesSchaumont
requested changes
Dec 13, 2024
| mdata = mudata.read(par["input"].strip()) | ||
| mod = mdata.mod[par["modality"]] | ||
|
|
||
| if "peak_annotation" not in mod.uns["atac"]: |
Member
There was a problem hiding this comment.
Could you create an argument for the location of the peaks?
Collaborator
Author
There was a problem hiding this comment.
This is the default value from muon: https://muon.readthedocs.io/en/latest/api/generated/muon.atac.tl.add_peak_annotation.html
Other muon functions check exactly this location, so if we store it somewhere else, the errors will appear
Member
There was a problem hiding this comment.
I think what we could do is add an argument here (with a default value peak_annotation) and also add this argument to other components where needed?
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Changelog
Add a component to calculate differentially accessible peaks for ATAC data.
Issue ticket number and link
Contributes to #398
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI tests succeed!