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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 AnnDataR6object from theanndatapackage, or anInMemoryAnnDataobject from theanndataR` package.

prepare_env

Whether to prepare and validate the Scanpy Python environment before conversion. Set to FALSE when a wrapper already prepared the environment and reticulate must keep the same 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
} # }