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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