Functionality to prepare matrix for NMF clustering + bug fixes #68
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mattssca
reviewed
Mar 30, 2022
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Good update Kostia. Regarding the bugs in dplyr pipes, that was completely my mistake. Accidentally swapped all "<-" for "=", thanks for catching this. As for the newly added function, would you consider expanding on the included example? It would've been nice to have an example df to work with as well, what do you think?
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Thanks Adam for a review and excellent suggestion! I have included a small matrix sample to be used as example and expanded the usage example with how to get it. It helped me to catch a bug where empty matrix was returned if there were no samples/features to drop. This has been addressed and is now ready for re-review. |
mattssca
approved these changes
Mar 31, 2022
This was referenced Apr 2, 2022
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In this PR:
massage_matrix_for_clusteringthat will take incoming data frame and output ready-to-go matrix for NMF. It reviews and squishes together CNV+SSM, cleans up overlaps between SSM and HOTSPOT features by giving priority to hotspot mutations, removes features not meeting cutoff for user-defined minimal occurrence, and removes samples without any feature.splendidHeatmapfunction as described in issue splendidHeatmap mismatches the features between clusters if metadata is not sorted #67dlpyrpipes.