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Load an AnnData Zarr store as a Seurat object

Source: R/LoadZarr.R
readZarr.Rd

Direct conversion from AnnData Zarr format (.zarr directory) to Seurat object. Supports zarr v2 stores as produced by Python anndata. This enables reading of cloud-native AnnData stores from CELLxGENE, Human Cell Atlas, and SpatialData workflows.

Usage

readZarr(
  file,
  assay.name = "RNA",
  verbose = TRUE,
  cache = TRUE,
  obs_idx = NULL,
  var_idx = NULL,
  layers = NULL,
  obsm = NULL,
  obsp = NULL,
  varm = NULL,
  varp = NULL,
  uns = NULL,
  include_x = TRUE,
  ...
)

Arguments

file

Path to a local .zarr directory, or a remote s3:///gs:// URL.

assay.name

Name for the primary assay (default: "RNA")

verbose

Show progress messages

cache

For remote URLs: TRUE to persist the download under tools::R_user_dir("scConvert", "cache"); FALSE to use a tempdir that is discarded with the R session. Ignored for local paths.

obs_idx, var_idx

Integer indices (1-based) selecting cells / features to keep. NULL (default) reads all. Index slicing pushes down to chunk fetches: only chunks of the cell / feature index, obs columns, obsm embeddings, var columns, and sparse indptr-resolved data blocks containing the requested indices are pulled.

layers

Character vector of /layers/* groups to read, or NULL (default) for all, or character(0) to skip all layers entirely. Skipping unused layers avoids their chunk fetches on remote stores.

obsm, obsp, varm, varp, uns

Same semantics as layers for the corresponding AnnData groups: NULL keeps everything, character() drops the entire group, otherwise reads only the named items.

include_x

If FALSE, skip reading the main expression matrix entirely. Useful for metadata-only reads from a remote store. Default TRUE. (If FALSE, a zero-row placeholder assay is constructed so the returned Seurat object still has the right number of cells.)

...

Additional arguments (currently unused)

Value

A Seurat object

Details

file may also be a remote URL: s3://bucket/key.zarr, gs://bucket/key.zarr. Anonymous (public) buckets only; private buckets requiring SigV4 signing are not supported. When cache is TRUE, the downloaded store is kept under tools::R_user_dir("scConvert", "cache") and reused on subsequent calls with the same URL.