Convert AnnData to SeuratObject using SeuratDisk/sceasy/scDIOR/schard/SeuratDisk+scDIOR.

Usage

AD2Seu(
  anndata.file,
  method = c("SeuratDisk", "sceasy", "scDIOR", "schard", "SeuratDisk+scDIOR"),
  assay = "RNA",
  load.assays = "RNA",
  slot = "counts",
  use.raw = TRUE
)

Arguments

anndata.file: The file contains AnnData.
method: Method used to perform conversion, choose from "SeuratDisk", "sceasy", "scDIOR", "schard", "SeuratDisk+scDIOR". Default: "SeuratDisk".
assay: Name to store assay data as. Default: RNA.
load.assays: Which assays to load, used when method is "SeuratDisk". Default: RNA.
slot: Slot to store adata.X, used when method is "sceasy". Default: counts.
use.raw: Logical value, whether to use adata.raw, used when method is "schard". Default: TRUE.

Value

A SeuratObject.

Examples

# SeuratDisk
ann.seu <- AD2Seu(anndata.file = "pbmc3k.h5ad", method = "SeuratDisk", assay = "RNA", load.assays = c("RNA"))
#> Error in AD2Seu(anndata.file = "pbmc3k.h5ad", method = "SeuratDisk", assay = "RNA",     load.assays = c("RNA")): pbmc3k.h5ad does not exist, please check!
# sceasy
ann.sceasy <- AD2Seu(anndata.file = "pbmc3k.h5ad", method = "sceasy", assay = "RNA", slot = "scale.data")
#> Error in AD2Seu(anndata.file = "pbmc3k.h5ad", method = "sceasy", assay = "RNA",     slot = "scale.data"): pbmc3k.h5ad does not exist, please check!
# scDIOR
ann.scdior <- AD2Seu(anndata.file = "pbmc3k.h5ad", method = "scDIOR", assay = "RNA")
#> Error in AD2Seu(anndata.file = "pbmc3k.h5ad", method = "scDIOR", assay = "RNA"): pbmc3k.h5ad does not exist, please check!
# schard
ann.schard <- AD2Seu(anndata.file = "pbmc3k.h5ad", method = "schard", assay = "RNA", use.raw = T)
#> Error in AD2Seu(anndata.file = "pbmc3k.h5ad", method = "schard", assay = "RNA",     use.raw = T): pbmc3k.h5ad does not exist, please check!
# SeuratDisk+scDIOR
ann.seuscdior <- AD2Seu(anndata.file = "pbmc3k.h5ad", method = "SeuratDisk+scDIOR", assay = "RNA", load.assays = c("RNA"))
#> Error in AD2Seu(anndata.file = "pbmc3k.h5ad", method = "SeuratDisk+scDIOR",     assay = "RNA", load.assays = c("RNA")): pbmc3k.h5ad does not exist, please check!