error when trying to overwrite a file

[vmedaert]

An error occurs in anndataR::from_Seurat with output_class="HDF5AnnData" when trying to write to an existing file:

Error in initialize(...) : 
obs must be NULL when loading an existing .h5ad file

[lazappi]

Can you please provide an example of the code you ran?

[vmedaert]

Can you please provide an example of the code you ran?

# load old seurat object
old <- readRDS("./rds/seuratObj3531889.rds")

# create seurat object v5
seuratObj <- CreateSeuratObject(
  counts = GetAssayData(old, layer="counts"),
  data = GetAssayData(old, layer="data"),
  meta.data = [email protected]
)
seuratObj <- SetAssayData(
  seuratObj,
  layer="scale.data",
  new.data=GetAssayData(old, layer="scale.data")
)
seuratObj@assays[["RNA"]]@layers$counts@Dimnames <- old@assays[["RNA"]]$counts@Dimnames
seuratObj@assays[["RNA"]]@layers$data@Dimnames <- old@assays[["RNA"]]$data@Dimnames
seuratObj[["RNA"]]@meta.data$gene <- old@assays[["RNA"]]$counts@Dimnames[[1]]

# this call throws the error if "./annData/annData3531889.h5" already exists (so I have to delete it to be able to update the file)
anndataR::from_Seurat(
  seuratObj,
  "HDF5AnnData",
  file="./annData/annData3531889.h5"
)