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Convert a Seurat object to an .h5ad file

Source: R/DataConvert.R
srt_to_h5ad.Rd

Convert a Seurat object to an .h5ad file

Usage

srt_to_h5ad(
  object,
  path,
  features = NULL,
  assay_x = "RNA",
  layer_x = "counts",
  assay_y = c("spliced", "unspliced"),
  layer_y = "counts",
  reductions = NULL,
  graphs = NULL,
  neighbors = NULL,
  convert_tools = FALSE,
  convert_misc = FALSE,
  overwrite = FALSE,
  verbose = TRUE,
  srt = NULL
)

Arguments

object

A Seurat object.

path

Path to the output .h5ad file.

features

Optional vector of features to include in the anndata object. Default is all features in assay_x.

assay_x

Assay to convert as the main data matrix in the anndata object.

layer_x

Layer name for assay_x in the Seurat object.

assay_y

Assays, or extra layers of assay_x, to convert as layers in the anndata object. Each name is matched against the assays of the object first, then against the layers of assay_x, which covers velocity matrices such as spliced and unspliced stored as layers of a Seurat v5 RNA assay.

layer_y

Layer names for the assays in assay_y. It is ignored for names that are matched as layers of assay_x, where the layer name itself is used.

reductions

Character vector specifying which Seurat reductions to convert into obsm. Default is NULL, which converts all available reductions.

graphs

Character vector specifying which Seurat graphs to convert into obsp. Default is NULL, which converts all available graphs.

neighbors

Character vector specifying which Seurat neighbor objects to convert into obsp. Default is NULL, which converts all available neighbor objects.

convert_tools

Whether to convert the tool-specific data.

convert_misc

Whether to convert the miscellaneous data.

overwrite

Whether to overwrite an existing file.

verbose

Whether to print the message. Default is TRUE.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

Invisibly returns the normalized path of the written file.

See also

srt_to_adata, h5ad_to_srt

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
srt_to_h5ad(pancreas_sub, "pancreas_sub.h5ad")
} # }