Convert SeuratObject to AnnData using SeuratDisk/sceasy/scDIOR.

Usage

Seu2AD(
  seu.obj,
  method = c("SeuratDisk", "sceasy", "scDIOR"),
  out.folder = NULL,
  out.filename = NULL,
  assay = "RNA",
  slot = "counts",
  save.scale = FALSE,
  conda.path = NULL
)

Arguments

seu.obj: A seurat object.
method: Method used to perform conversion, choose from "SeuratDisk", "sceasy", "scDIOR". Default: "SeuratDisk".
out.folder: Output folder. Default: NULL (current working directory).
out.filename: Output file name, e.g., test.h5ad. Default: NULL (seu.obj name, method, h5ad.).
assay: Assay name to store expression matrices in SeuratObject. Default: RNA.
slot: Slot for adata.X, used when method is "sceasy". Default: counts.
save.scale: Logical value, whether to save scaled count matrix, used when method is "SeuratDisk", "scDIOR". Default: FALSE. When method is "SeuratDisk" and save.scale is TRUE (FALSE), scaled data is stored in X， log-normalized data is in raw.X (log-normalized data is stored in X，raw count matrix is in raw.X); When method is "scDIOR" and save.scale is TRUE (FALSE), scaled data is stored in X，log-normalized data is in raw.X, raw count matrix is in layers (log-normalized data is stored in X，raw count matrix is in layers).
conda.path: Conda environment path, used when method is "sceasy". Default: NULL.

Value

Run log.

Examples

# SeuratDisk
Seu2AD(seu.obj = pbmc3k.final, method = "SeuratDisk", out.folder = "benchmark", assay = "RNA", save.scale = TRUE)
#> Error in Seurat::GetAssayData(object = seu.obj, slot = "scale.data", assay = assay): object 'pbmc3k.final' not found
# sceasy
Seu2AD(seu.obj = pbmc3k.final, method = "sceasy", out.folder = "benchmark", assay = "RNA", slot = "counts", conda.path = "/path/to/conda")
#> Error in reticulate::use_condaenv(conda.path, required = TRUE): Unable to locate conda environment '/path/to/conda'.
# scDIOR
Seu2AD(seu.obj = pbmc3k.final, method = "scDIOR", out.folder = "benchmark", assay = "RNA", save.scale = TRUE)
#> There is an error when using scDIOR: Error in seurat_write_h5(seurat = data, file = file, assay.name = assay.name, : object 'pbmc3k.final' not found
#> NULL