[Bioc-devel] transitioning scater/scran to SingleCellExperiment

Angerer, Philipp philipp.angerer at helmholtz-muenchen.de
Tue Aug 8 11:48:19 CEST 2017

Hi Aaron and Martin, 

In any case, a distance matrix calculated from such an array would be fine, as long as the dimensions are equal to the number of cells. The question is whether it is needed by enough packages to warrant a slot in the base SCE class; I will discuss this with Davide and Vlad. 

Yeah, that was my point. since it’s cumbersome and non-natural to have 3D data in there, a distance matrix would fit better. 

The SingleCellExperiment package makes no statement on whether downstream users/packages want to (or not) use the tidy-verse or ggplot2. It simply provides the minimal class and methods; convenience wrappers are left to the discretion of each package developer. scater, for example, implements a few dplyr verbs for SCE objects. 

Of course, but only fortify is ggplot2-specific. But anyway; Martin pointed out: 

FWIW, SummarizedExperiment (hence SingleCellExperimet) uses $ (and $<-; also [[ and [[<-) to access (with auto-completion) colData. And it wouldn't be a good idea to have $ access one element (counts) and $<- modify another (rowData), or to mix what $ and [[ access. 


Ah, I see! names and .DollarNames.SummarizedExperiment are also defined! Well, that’s good enough i think, although this seems cumbersome: 
assays(sce)$log_counts[ 'Actb' , ] 

Cheers, Phil 


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