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get_DE_genes with different celltype.id parameter #1

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scseeman opened this issue Apr 1, 2022 · 0 comments
Open

get_DE_genes with different celltype.id parameter #1

scseeman opened this issue Apr 1, 2022 · 0 comments

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@scseeman
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scseeman commented Apr 1, 2022

Hi,
First, thank you for the tutorials included with this package, I find them extremely helpful and have been able to implement most of your code on my data. I was however trying to use get_DE_genes setting the celltype.id to something other than "celltype". My SCE object has "cluster" as one of the columns in colData yet when I set celltype.id = "cluster" I get the following error:
image

"cluster" in sce_data:
image

When I investigated the .check_celltype_in_sce it looks like "celltype" is hardcoded in? I am also new to coding in R (mostly used Python in the past) so apologies if that is not the issue. Thanks for the help.

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