Milo-object check in assign_neighborhood misses milo-objects
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Dear all,
Thank you for the great package.
I want use miloDE with a milo-object previously constructed with miloR (to use BPPARAM, BSPARAM, etc.).
The source code in https://github.com/MarioniLab/miloDE/blob/main/R/assign_neighbourhoods.R at line 68 uses if (is(x , "SingleCellExperiment")), where x is the input SingleCellExperiment and/or Milo-object.
I believe the problem is, that a milo-object is still a SingleCellExperiment (is(milo.obj, "SingleCellExperiment") == TRUE) therefore the function continues to construct a new neighborhood graph even though the input is a milo-object with existent graph.
In some trial and error i found is(milo.obj, "SingleCellExperiment") && !is(milo.obj, "Milo") to be the best check here.
Would it be alright to test this and possibly update?
Thank you and best regards,
Max
@MaximilianNuber I'm sorry, I completely missed this issue - I will do some tests and update shortly - but yeah, your suggestion seems to be a good fit
@MaximilianNuber fixed and thanks for bringing it to my attention (and sorry for replying so late, this notification completely slipped through me)