Error while trying to convert SeuratObj to Anndata

[jovanakalamkovic99]

Hello,

I am encountering a problem when trying to convert the Seurat object obtained from PRECAST into Anndata.
Firstly, I perform PRECAST on two samples that were prepared from anndatas and transformed into seurat objects using the library sceasy (https://github.com/cellgeni/sceasy). After performing PRECAST, I perform SelectModel and then IntegrateSpaData.
After the last function is performed the result is a seurat object (before that it is a PRECAST object).

The last thing I want to do is to return the data to an Anndata for further processing (namely, I want to calculate the Integration LISI score and some ARI scores) for which I need the whole object. I tried running:

sceasy::convertFormat(seuInt, from="seurat", to="anndata", assay = "PRE_CAST",
outFile='mouse_brain_precast/PRECAST_BRAIN.h5ad')

The assay is a parameter because the default assay is named RNA and after the IntegrateSpaData the assay is named PRE_CAST.

However, after attempting to convert the format using sceasy I get an error
Error in ncol(df) :
no slot of name "meta.features" for this object of class "Assay5"
Calls: -> func -> .regularise_df -> ncol

And upon inspection I do see that the slot meta.features is not there, but I cannot create it because whenever I try to create the meta.features I get the following error:

Error in (function (cl, name, valueClass) :
‘meta.features’ is not a slot in class “Seurat”

Please help me solve this problem or find a workaround.
Thank you!

[jovanakalamkovic99]

I believe I have found the solution thanks to @haukeh90 on (cellgeni/sceasy#76)

Leukocytes[["RNA3"]] <- as(object = Leukocytes[["RNA"]], Class = "Assay")
DefaultAssay(Leukocytes) <- "RNA3"
Leukocytes[["RNA"]] <- NULL
Leukocytes <- RenameAssays(object = Leukocytes, RNA3 = 'RNA')