no applicable method for 'JoinLayers' applied to an object of class "c('Assay', 'KeyMixin')

[DLY-2021]

In Seurat V5 using hdWGCNA, I encountered the following issue: 'Error in UseMethod(generic = "JoinLayers", object = object) : no applicable method for 'JoinLayers' applied to an object of class "c('Assay', 'KeyMixin')"'. The code is: 'seurat_obj <- MetacellsByGroups(
seurat_obj = seurat_obj,
reduction = "harmony",
assay = 'SCT',
slot = 'counts')'

[smorabit]

Hi,

Not sure what this "KeyMIxin" assay is, I haven't seen this before. It looks like this is an error thrown by Seurat rather than hdWGCNA itself, unfortunately we run into a lot of errors related to Seurat v5 since they decided to change the SeuratObject.

I am wondering if the code works when you use assay='RNA' instead of 'SCT'. If you have a reproducible example of this error it would be easier for me to look into it.

[professor-sagittarius]

Hi Sam,

I encountered the same error. Here's a reproducible example using the Seurat object in this .qs file

Notably, the error occurs with non-SCT data. I have successfully performed hdWGCNA on other similar datasets, but the error has only occurred with this one. The object in the .qs has been downsampled, but the error still occurs with the full dataset.

obj <- qs::qread("joinLayersError")

obj <- SetupForWGCNA(
    obj,
    gene_select = "fraction", # the gene selection approach
    group.by = "cell_type",
    fraction = 0.05 # fraction of cells that a gene needs to be expressed in order to be included
)

obj <- MetacellsByGroups(
    obj,
    group.by = c("cell_type"), # specify the columns in [email protected] to group by
    reduction = 'harmony', # select the dimensionality reduction to perform KNN on
    k = 25, # nearest-neighbors parameter
    max_shared = 10, # maximum number of shared cells between two metacells
    min_cells = 100, 
    ident.group = 'cell_type', # set the Idents of the metacell seurat object
    verbose=T
)

Error in UseMethod(generic = "JoinLayers", object = object) : 
  no applicable method for 'JoinLayers' applied to an object of class "c('Assay', 'KeyMixin')"

[connorclouddevine]

Hi all,

I found a workaround for this problem:

satijalab/seurat#7672 (comment)

I was loading RDS output from a pipeline and I suspect they may be v3 objects which are mysteriously incompatible with JoinLayers; I received the same error when running JoinLayers on a Seurat object. This block of code fixed the above error.

assay5 <- as(pbmc[["RNA"]], Class = "Assay5")
seurat5 <- CreateSeuratObject(assay5, meta.data = [email protected])

seurat5 <- JoinLayers(seurat5)

[Skye-lulu]

Hi all,
I solve this on my computer by downgrade the igraph version to 2.0.3