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Convert a Seurat object to an AnnData object

Source: R/DataConvert.R
srt_to_adata.Rd

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",
  layer_x = "counts",
  assay_y = c("spliced", "unspliced"),
  layer_y = "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 in the anndata object. Default is "RNA".

layer_x

Layer name for assay_x in the Seurat object. Default is "counts".

assay_y

Assays to convert as layers in the anndata object. Default is c("spliced", "unspliced").

layer_y

Layer names for the assay_y in the Seurat object. Default is "counts".

convert_tools

Whether to convert the tool-specific data. Default is FALSE.

convert_misc

Whether to convert the miscellaneous data. Default is FALSE.

verbose

Whether to print the message. Default is TRUE.

Value

A anndata object.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
adata <- srt_to_adata(pancreas_sub)
adata

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