Add atac_marker_peaks component #879
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DriesSchaumont
requested changes
Dec 13, 2024
| mdata = mudata.read(par["input"].strip()) | ||
| mod = mdata.mod[par["modality"]] | ||
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| if "peak_annotation" not in mod.uns["atac"]: |
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Could you create an argument for the location of the peaks?
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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
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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?
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Changelog
Add a component to calculate differentially accessible peaks for ATAC data.
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Contributes to #398
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Proposed changes are described in the CHANGELOG.md
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