Load a Loom file as a Seurat object

Load gene expression data from Loom files (HDF5-based file format for storing annotated matrices) into a Seurat object. Loom files are commonly created by Python-based analysis tools and offer an alternative to H5AD format for storing single-cell data.

Usage

LoadLoom(
  file,
  assay = NULL,
  cells = "CellID",
  features = "Gene",
  normalized = NULL,
  scaled = NULL,
  filter = c("cells", "features", "all", "none"),
  verbose = TRUE,
  ...
)

# S3 method for class 'character'
LoadLoom(file, ...)

# S3 method for class 'H5File'
LoadLoom(file, ...)

# S3 method for class 'loom'
LoadLoom(file, ...)

# S3 method for class 'loom'
as.Seurat(
  x,
  assay = NULL,
  cells = "CellID",
  features = "Gene",
  normalized = NULL,
  scaled = NULL,
  filter = c("cells", "features", "all", "none"),
  verbose = TRUE,
  ...
)

Arguments

file, x: Name of Loom file (character path) or a loom object connection to load data from
assay: Name of assay to store expression data as. If NULL, will search for an HDF5 attribute named SEURAT_ASSAY or dataset at /attrs/SEURAT_ASSAY for the assay name. Defaults to "RNA" if not found.
cells: Name of dataset in /col_attrs containing cell/sample names. If not found, uses column indices as cell names.
features: Name of dataset in /row_attrs containing feature/gene names. If not found, uses row indices as feature names.
normalized: Name of layer in /layers to load as normalized expression data; special value "/matrix" loads the main matrix as normalized data instead of counts
scaled: Name of layer in /layers to load as scaled data
filter: Logical; if TRUE, keep only cells and features marked as valid using /col_attrs/Valid and /row_attrs/Valid attributes
verbose: Logical; if TRUE (default), show progress updates
...: Arguments passed to other methods

Value

A Seurat object containing the expression matrix and metadata from the Loom file

Details

The Loom format stores data in a specific HDF5 structure:

/matrix: Main expression matrix (features x cells)
/row_attrs: Feature-level metadata (gene names, coordinates, etc.)
/col_attrs: Cell/sample-level metadata
/layers: Additional expression layers (normalized, scaled, etc.)

Loom 0.1 Loading

Loading data from loom files less than version 3.0.0 is not currently supported

Loom 3.0.0 Loading

For loom files version 3.0.0 and higher, LoadLoom3.0 provides comprehensive loading with support for filtering, dimensional reductions, and cell graphs.

Examples

if (FALSE) { # \dontrun{
library(SeuratDisk)

# Load a basic Loom file
seurat_obj <- LoadLoom("data.loom")

# Load with specific assay name
seurat_obj <- LoadLoom("data.loom", assay = "RNA")

# Load and filter to valid cells/features only
seurat_obj <- LoadLoom("data.loom", filter = TRUE)

# Load specific layers
seurat_obj <- LoadLoom(
  "data.loom",
  normalized = "normalized",
  scaled = "scaled"
)
} # }