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Convert an anndata object to a seurat object

Source: R/DataConvert.R
adata_to_srt.Rd

Convert an anndata object to a seurat object

Usage

adata_to_srt(adata, prepare_env = TRUE, verbose = TRUE)

Arguments

adata

An AnnData object. Can be a Python AnnData object (from scanpy/reticulate), an AnnDataR6 object from the anndata package, or an InMemoryAnnData object from the anndataR package.

prepare_env

Whether to prepare and validate the Scanpy Python environment before conversion. Wrapper functions that already prepared the environment should pass FALSE to keep one reticulate binding.

verbose

Whether to print the message. Default is TRUE.

See also

srt_to_adata

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
adata <- srt_to_adata(pancreas_sub)
adata <- RunPAGA(
  adata = adata,
  group.by = "SubCellType",
  linear_reduction = "X_pca",
  nonlinear_reduction = "X_umap"
)
srt <- adata_to_srt(adata)
srt

# Or convert a h5ad file to Seurat object
sc <- reticulate::import("scanpy")
adata <- sc$read_h5ad("pancreas.h5ad")
srt <- adata_to_srt(adata)
srt
} # }