AnswerBun.com

Changing active.ident in Seurat

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..

One Answer

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

Add your own answers!

Related Questions

Sequence alignment using BWT

1  Asked on December 5, 2021

   

Generating 3D coordinates error

1  Asked on December 2, 2021

   

Seurat DE t.test

1  Asked on December 2, 2021

       

Extract sequences from partial Header

2  Asked on November 24, 2021

     

Viral Metagenomics

1  Asked on November 10, 2021

     

Ask a Question

Get help from others!

© 2023 AnswerBun.com. All rights reserved. Sites we Love: PCI Database, MenuIva, UKBizDB, Menu Kuliner, Sharing RPP, SolveDir