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. 
BQ_BEGIN


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. 
BQ_END


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


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. 

Martin 
BQ_END


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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