Manually change root directory after creating BP cell Seurat object

[Dazcam]

Hi there,

I have been running an analysis in Seurat 5 that is partially run on a local machine and a remote server.

As my Seurat objects were created remotely using write_matrix_dir(), after moving these objects to my local machine, when trying to run some functions locally I encounter errors as the root directory for the counts data is set to the remote location not the local directory (note that I have the large counts files stored locally and remotely):

> VlnPlot(seurat_object, general_genes, stack = TRUE, flip = TRUE, same.y.lims = TRUE)

#> Error in (function (cond)  : 
#>   error in evaluating the argument 'x' in selecting a method for function 'as.matrix': Missing directory: 
#>   /scratch/xxxxxx/results/01R_objects/CBL_BP

Is there a simple way to change the root directory that the Seurat object points to? I can't put my finger on where it is stored in the Seurat object.

Many Thanks.

[shnatova]

Hi @Dazcam any updates on how you overcame this? I am struggling with the same, using an object created locally and transfered to a remote server

[Dazcam]

Hi @Dazcam any updates on how you overcame this? I am struggling with the same, using an object created locally and transfered to a remote server

Not yet @shnatova. I've posted a follow up question on the SeuratObject GitHub to see if I can get a response there.