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Convert Seurat rds file to AnnData h5ad file

Source: R/RPyCall.R
rds2h5ad.Rd

Converts a Seurat rds file to a Python AnnData h5ad file for use with scanpy and other Python-based tools.

Usage

rds2h5ad(
  seurat_obj = NULL,
  data_type = "stRNA",
  convert_mode = "seurat",
  assay_id = NULL,
  grp_nm = NULL,
  dir_nm = "M0_rds2h5ad"
)

Arguments

seurat_obj

A Seurat object to convert

data_type

Character, data type - "stRNA" (spatial) or "scRNA" (single-cell) (default: "stRNA")

convert_mode

Character, conversion method - "seurat" (using SeuratDisk) (default: "seurat")

assay_id

Character, assay name to convert (default: NULL, auto-detected)

grp_nm

Character, group name for output organization (default: NULL)

dir_nm

Character, directory name for output (default: "M0_rds2h5ad")

Value

NULL (invisible), saves h5ad file to disk

Examples

if (FALSE) { # \dontrun{
# Convert Seurat object to h5ad
configure_conda()
rds2h5ad(
  seurat_obj = seurat_object,
  data_type = "stRNA",
  grp_nm = "sample1"
)
} # }