no slot of name "data" for this object of class "Assay5"

[Rohit-Satyam]

Dear @praneet1988 @kthorner

I am trying to use your package to annotate the query scrnaseq of plasmodium falciparum. I have integrated object, which I subset for use with your package function

reftemp <- subset(integrate, Sample %in% c("MCA"))
query<- subset(integrate, Sample %in% c(integrate$Sample %>% unique() %>% .[1:4]))

out.CelltypeAnnotation = CelltypeAnnotation(reference = reftemp, query = query, downsample = FALSE, validatePredictions = FALSE, annotationCol = "STAGE_HR2")
Setting Assay of reference and query to RNA
Running Diagonistis on reference and query
Number of cells in reference:28659
Number of cells in query:25166
Calculating ratio of number of cells in reference vs query
Ratio of number of cells in query vs reference:0.878118566593391
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
  |=========================================================================================================| 100%
Warning: Different features in new layer data than already exists for scale.data
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
  |=========================================================================================================| 100%
Warning: Different features in new layer data than already exists for scale.data
Finding common variable features between reference and query
Subsetting reference and query for common variable features
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Preparing train and test datasets from reference and query
Error in CelltypeAnnotation(reference = reftemp, query = query, downsample = FALSE,  : 
  no slot of name "data" for this object of class "Assay5"

[Rohit-Satyam]

This stems from using reference_use[["RNA"]]@data rather than reference_use[["RNA"]]$data as per new Seurat v5 architecture.

Also, what's the difference between CelltypeAnnotation and LabelHarmonization ? Which one should I use to transfer labels from reference to query?

[Rohit-Satyam]

@bschilder @praneet1988 @kthorner did you guys update this?