Convert SingleCellExperiemnt to AnnData using sceasy/scDIOR/zellkonverter.

Usage

SCE2AD(
  sce.obj,
  method = c("sceasy", "scDIOR", "zellkonverter"),
  out.folder = NULL,
  out.filename = NULL,
  slot = "counts",
  conda.path = NULL
)

Arguments

sce.obj: A SingleCellExperiment object.
method: Method used to perform conversion, choose from "sceasy", "scDIOR", "zellkonverter". Default: "sceasy".
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.).
slot: Slot for adata.X, used when method is "sceasy", "zellkonverter". Default: counts.
conda.path: Conda environment path, used when method is "zellkonverter" or "sceasy". Default: NULL.

Value

Run log.

Examples

# sceasy
SCE2AD(sce.obj = pbmc3k.sce, method = "sceasy", out.folder = "benchmark", slot = "rawcounts", conda.path = "/path/to/conda")
# scDIOR
pbmc3k.sce.scdior <- pbmc3k.sce
library(SingleCellExperiment)
# scDIOR does not support varm in rowData
rowData(pbmc3k.sce.scdior)$varm <- NULL
SCE2AD(sce.obj = pbmc3k.sce.scdior, method = "scDIOR", out.folder = "benchmark")
# zellkonverter
SCE2AD(sce.obj = pbmc3k.sce, method = "zellkonverter", out.folder = "benchmark", slot = "rawcounts", conda.path = "/path/to/conda")