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I have been running an analysis in Seurat 5 that is partially run on a local machine and a remote server, and I've been trying to work out how to change the address of where the BP cell generated count matrices are located. After moving Seurat objects generated remotely to my local machine, I encounter errors when trying to run certain functions as the root directory for the count data is set to the remote directory, rather than the local directory. See here for more details.
The SaveSeuratRds() function looks as if it may be able to change this directory address, but there does not appear to be functionality to just change it without moving the on-disk layers from their original location. I've tried running SaveSeuratRds() with move = F, but when you reload the object the layers are missing:
I've also tried digging around the Seurat Object, but I can't put my finger where this address is stored. The best I could do was find a list of 28 identical items containing the following, but I'm not convinced this is worth changing as it looks like a log:
Dazcam
changed the title
SaveSeuratRds(): Is there a way to alter root directory of Seurat object
SaveSeuratRds(): Is there a way to alter directory address of 'on-disk' matrices in Seurat object
Apr 9, 2024
Hello,
I have been running an analysis in Seurat 5 that is partially run on a local machine and a remote server, and I've been trying to work out how to change the address of where the BP cell generated count matrices are located. After moving Seurat objects generated remotely to my local machine, I encounter errors when trying to run certain functions as the root directory for the count data is set to the remote directory, rather than the local directory. See here for more details.
The
SaveSeuratRds()
function looks as if it may be able to change this directory address, but there does not appear to be functionality to just change it without moving the on-disk layers from their original location. I've tried runningSaveSeuratRds()
withmove = F
, but when you reload the object the layers are missing:When running
SaveSeuratRds()
withmove = T
, obviously the original path is not found (this also occurs when settingrelative = T
orrelative = F
).I've also tried digging around the Seurat Object, but I can't put my finger where this address is stored. The best I could do was find a list of 28 identical items containing the following, but I'm not convinced this is worth changing as it looks like a log:
Matrix_list
So a couple of questions then:
SaveSeuratRds()
or otherwise?SaveSeuratRds()
to handle local / remote analyses?Many thanks.
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