Comments (5)
Hi again
I tried several things randomly:
it seems that "getAssaData" is deprecated in Seurat5 and to be replaced with LayerData, so could my problem come from incompatibility between Seurat5 and ScMega ?
I try to run LayerData for each assay (chromvar, RNA and ATAC), if I run them alone, I got nothing different, if I run for each something like :
objG[['RNA']] <- as(objG[['RNA']], Class = 'Assay5')
LayerData(object = objG[['RNA']])
I have a different error message: no motifs name in this Assay5 object. The problem arises only when I transform the ATAC assay in Assay5, not when I keep a "ChromatinAssay" class, but sadly then I have the "GetAssayData()`:
! No layers are found" again.
Don't know if that help ?
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If ever it can help someone, here is what I did :
I bypassaded the getassayy using layerdata function:
objG[['SoupXRNA']] <- as(objG[['SoupXRNA']], Class = 'Assay5')
LayerData(object = objG[['SoupXRNA']])
objG[['ATAC']] <- as(objG[['ATAC']], Class = 'ChromatinAssay')
LayerData(object = objG[['ATAC']])
objG[['chromvar']] <- as(objG[['chromvar']], Class = 'ChromatinAssay')
LayerData(object = objG[['chromvar']])
Class = 'ChromatinAssay is necessary to keep the motif names
then I copied the selectTFs function to run if in the rstudio interface directly with some modifications:
- replace RNA assay with SoupXRNA as I had to run soupX to clean my data
- and increment the motif names call solution proposed by @AmandaKedaigle in the issue " Motif matching when using mouse data #18 "
and It seems to work fine
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Hi @Dalhte
Sorry for my late reply and glad that you found a solution.
Indeed, the Seurat v5 has uplated many APIs, and I need some time to update scMEGA to keep them compatible.
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Hi @lzj1769
Don't worry, it was nice to find a solution by myself :) Even if the solution is quite tedious :DDD
Best
David
from scmega.
Hello!
Many thanks for the tool,
I am also encountering this same error with the issue seeming to be with GetAssayData()
in GetTrajectory
. I have had a go at trying to bypass this issue as @Dalhte suggested but this is just creating more errors. Could you please suggest a workaround for this or perhaps a suggestion of which Seurat version is best used with scMEGA? I followed the installation instructions which says devtools::install_github("satijalab/seurat", "seurat5", upgrade='always')
, should I try re-running the scMEGA steps but with an older version of seurat? Any suggestions are greatly appreciated, I have managed to follow the steps of the tutorial up to SelectTFs
so I'm very keen to get this final bit working to build the GRN!
Eva
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Related Issues (20)
- get the gene activity matrix from ArchR HOT 2
- Using scMEGA for two treatment groups? HOT 2
- snATAC data does not have a $Harmony dimension reduced matrix HOT 1
- Error for Install package
- Error in Running SelectTFs HOT 3
- Big data takes too long for cells to pair HOT 2
- SelectGenes use other genome HOT 2
- Motif matching when using mouse data HOT 6
- Use obj.pair to show the expression of marker gene HOT 1
- script for preparing data HOT 1
- NetCentPlot error HOT 4
- The use of Co-embedding function HOT 2
- Incompability with Seurat v5
- error in SelectTFs or GetTrajectory HOT 1
- AddTargetAssay HOT 2
- CoembedData - Error: None of the provided refdata elements are valid.
- get cell type-specific peak
- Why CreatePairedObject is not working?
- GRNSpatialPlot HOT 2
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