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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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Excluding principal components from clustering #71

Closed martabrozynska closed 6 years ago

martabrozynska commented 6 years ago

Hi, Would it be possible to exclude a specific principal component (PC) from the clustering using SC3? What I'd like to do is to run the clustering on PCs without the PC1 (it explains a variation I'm not interested in). Hope it makes sense. Thanks!

CodeInTheSkies commented 6 years ago

Hi @martabrozynska , I'm not attempting to answer your question but rather it looks like you can answer one of my questions that I posted earlier here: https://github.com/hemberg-lab/SC3/issues/75

Basically, I would like to know if one can run SC3 clustering on PCs rather than the expression matrix. It looks like you have done this, correct?

If so, could you please let me know what's the correct way to do this? I mean the steps, at what point can one bring in the PC data (from Seurat, for e.g.), etc.

Thanks in advance for your response.

wikiselev commented 6 years ago

Hi, sorry for a long delay. I think the answer to the original question is no, in the current implementation the first n principal components are used for clustering and there is no parameter controlling your preferred behaviour. However, you can manually remove components from the metadata(sce)$sc3$transformations matrices. See more details here.