pcaExplorer on PCA from Seurat

[lucygarner]

Hi,

Is there a way to use pcaExplorer with the DimReduc object from Seurat (i.e. convert this into a suitable format)? Or would I need to run prcomp?

Best wishes,
Lucy

[federicomarini]

Hi Lucy,
Using directly the SeuratObject is not possible at the moment.
A workaround: convert that object to a SummarizedExperiment/SingleCellExperiment, and then use those results as input?
Considering that the development of pcaExplorer started way before Seurat (and single cell data 😛 ), it might mean quite a large piece of work to refactor/allow that input.
Sorry I do not have a better answer!
Federico

[lucygarner]

Thanks @federicomarini. No worries, I just wanted to check. I was looking at the hi_loadings function but it says the input is a prcomp object. Can you also supply a SingleCellExperiment object?

I have currently written my own version of the function that extracts the loadings from a Seurat object instead.

[federicomarini]

Hm, same as for pcaExplorer() - that works on a DESeqDataSet mainly, so all things use to be computed at runtime (which was never a large deal with the "classical" small bulk RNA-seq datasets...).
Probably you are best served if you stick to the Seurat framework, I have the impression it might cover a few things you would do with pcaExplorer - well, of course, not in the context of a nicely designed app 😉

[lucygarner]

Yes, datasets are a bit larger now! Thanks for the quick response.