srt_to_adata: Convert a seurat object to an anndata object using reticulate

In zh542370159/SCP: Single Cell Pipeline

Convert a seurat object to an anndata object using reticulate

Description

This function takes a Seurat object and converts it to an anndata object using the reticulate package.

Usage

srt_to_adata(
  srt,
  features = NULL,
  assay_X = "RNA",
  slot_X = "counts",
  assay_layers = c("spliced", "unspliced"),
  slot_layers = "counts",
  convert_tools = FALSE,
  convert_misc = FALSE,
  verbose = TRUE
)

Arguments

srt	A Seurat object.
features	Optional vector of features to include in the anndata object. Defaults to all features in assay_X.
assay_X	Assay to convert as the main data matrix (X) in the anndata object.
slot_X	Slot name for assay_X in the Seurat object.
assay_layers	Assays to convert as layers in the anndata object.
slot_layers	Slot names for the assay_layers in the Seurat object.
convert_tools	Logical indicating whether to convert the tool-specific data.
convert_misc	Logical indicating whether to convert the miscellaneous data.
verbose	Logical indicating whether to print verbose messages during the conversion process.

Value

An anndata object.

A anndata object.

Examples

data("pancreas_sub")
adata <- srt_to_adata(pancreas_sub)
adata

### Or save as an h5ad file or a loom file
# adata$write_h5ad("pancreas_sub.h5ad")
# adata$write_loom("pancreas_sub.loom", write_obsm_varm = TRUE)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.