Hi friendly Bioc gang! I'm struggling with what seems like a silly problem. I'm
trying to write a simple wrapper S4 generic that accesses the data slot of
various S4 objects (seurat and SingleCellExperiment objects). So the generic is:
setGeneric("getGE",function(x) standardGeneric("getGE"))
And the methods are:
setMethod("getGE","seurat",
function(x) Seurat::GetAssayData(x))
setMethod("getGE","SingleCellExperiment",
function(x) SingleCellExperiment::logcounts(x))
Problem is that when I install the package, I get the warning
> in method for �getGE� with signature �"seurat"�: no definition for class
> �seurat�
This isn't surprising, since Seurat isn't imported, but I don't want the user
to have to import it if their data is in a SingleCellExperiment object. The
function still seems to work fine if I attach Seurat and load a seurat object,
so I'm tempted to just suppress the error (but darned if I know how to do that
either). Before I do something so rash, does anyone have a suggestion for a
less dumb way to do this?
Thanks so much!
Brendan
www.baderlab.org/BrendanInnes<http://www.baderlab.org/BrendanInnes>
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