multiSpecificity() Not compatible with seurat v5

[DrGin-hub]

Here the error

multiSpecificity(object = seurat_object_v5)

Error in getExpressionMatrix(object, which.data = "data") :
no slot of name "data" for this object of class "Assay5"

I think an update in the package to make it compatible with Seurat v5 would be great

[simran-9849]

Hii,
I'm running into the same issue when trying to use func multiSpecificity() for seurat object v5. Can you please let me know how you fixed the issue if you could? Appreciate your help!

Thank you

[Mayank0512]

Hii,

I was facing the same issue. If the default assay is set to SCT the GetAssayData on which the getExpressionMatrix(object, which.data = "data") depends works and the error is resolved for me!

Incase SCT is not what you prefer and you have your normalized data stored differently, you can modify the function easily by just changing how you access the data. Doing this should be easy, write the same function as on GitHub of scMiko for getExpressionMatrix by updating the way to access the data and then use the following commands to overwrite the existinbg function in scMiko :-

Override the package function

unlockBinding("getExpressionMatrix", asNamespace("scMiko"))
assign("getExpressionMatrix", getExpressionMatrix, envir = asNamespace("scMiko"))
lockBinding("getExpressionMatrix", asNamespace("scMiko))

Hope this helps!