Import an .h5ad file as a Seurat or SingleCellExperiment object

A single entry point that reads adata.X (or adata.raw.X), adata.obs, adata.var and adata.obsm and assembles either a Seurat or a SingleCellExperiment. A missing adata.raw downgrades gracefully to adata.X with a warning rather than failing.

Usage

quasar_h5adimport(
  filename,
  as = c("seurat", "sce"),
  use.raw = TRUE,
  load.X = TRUE,
  load.obsm = TRUE,
  assay = "RNA",
  verbose = TRUE
)

Arguments

filename

path to the .h5ad file.

as

one of "seurat" or "sce"; the object type to return.

use.raw

logical, default TRUE. Use adata.raw.X / adata.raw.var when present, otherwise adata.X / adata.var.

load.X

logical, whether to load the expression matrix. If FALSE an all-zero sparse matrix of the right shape is used (much faster).

load.obsm

logical, whether to load adata.obsm as reduced dimensions / DimReducs.

assay

Seurat assay name to populate (ignored for as = "sce").

verbose

logical, print a start line and a summary block.

Value

a Seurat or SingleCellExperiment object.

Examples

if (FALSE) { # \dontrun{
## Round-trip on tiny data: write a small bulk matrix, then read it back.
f   <- tempfile(fileext = ".h5ad")
mat <- matrix(rpois(15 * 8, 2), nrow = 15,
              dimnames = list(paste0("gene", 1:15), paste0("cell", 1:8)))
quasar_h5adexporter(mat, f, bulk_orientation = "genes_x_samples")

sce <- quasar_h5adimport(f, as = "sce",    use.raw = FALSE)
seu <- quasar_h5adimport(f, as = "seurat", use.raw = FALSE)
} # }