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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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Functionality to prepare matrix for NMF clustering + bug fixes #68

Closed Kdreval closed 2 years ago

Kdreval commented 2 years ago

In this PR:

  1. Added new function massage_matrix_for_clustering that 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.
  2. Bug fixes in splendidHeatmap function as described in issue #67
  3. Added more lymphoma genes and harmonized it with the grch37, hg38 bed files of lymphoma genes as described in issue #66
  4. Other small bug fixes related to handling of row/column names in dlpyr pipes.
Kdreval commented 2 years ago

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.