Bioinformatics Asked on August 31, 2021
Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn’t. I don’t understand how to fix it?
[email protected] <- [email protected]$status
Error in (function (cl, name, valueClass) :
assignment of an object of class “character” is not valid for @‘active.ident’ in an object of class
“Seurat”; is(value, "factor") is not TRUE
head([email protected])
orig.ident nCount_RNA nFeature_RNA percent.mito status RNA_snn_res.0.6 seurat_clusters
BC03_03 BC03 998414.7 3356 0.07869098 nonTumor 0 0
BC03_09 BC03 999853.6 7616 0.12964336 primary 0 0
BC03_13 BC03 998206.5 8457 0.17672205 primary 0 0
BC03_17 BC03 999535.1 7494 0.11323008 primary 0 0
I want to run the UMAP with the clusters named according to the status and not seurat clusters.However, the code isnt working..
M <- SetIdent(M, value = "status")
or more explicitly
M <- SetIdent(M, value = [email protected]$status)
You can also use the group.by argument of UMAPPlot() or other plotting functions from Seurat for that matter.
Answered by haci on August 31, 2021
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