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Update tree agglomeration #656

Merged
merged 7 commits into from
Nov 5, 2024
Merged

Update tree agglomeration #656

merged 7 commits into from
Nov 5, 2024

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TuomasBorman
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@TuomasBorman TuomasBorman commented Nov 5, 2024 •
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Add tree agglomeration to subsetByPrevalent() and subsetByRare(). Fixes this issue: #198

Update the tree agglomeration; we used own implementation in agglomerateBy*() functions but now we utilize TreeSummarizedExperiment::subsetByLeaf(). Own implementation is still used in functions that handle matrix and tree, not TreeSE object.

@TuomasBorman TuomasBorman linked an issue Nov 5, 2024 that may be closed by this pull request
Add tree collapse to subsetByPrevalentTaxa and other related methods #198
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@TuomasBorman TuomasBorman mentioned this pull request Nov 5, 2024
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@TuomasBorman TuomasBorman merged commit 56cce49 into devel Nov 5, 2024
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@TuomasBorman TuomasBorman deleted the update_tree_agglomeration branch November 5, 2024 08:07
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Add tree collapse to subsetByPrevalentTaxa and other related methods
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@TuomasBorman