Loom-file Loading

Version-specific loom-file loading functions

Usage

LoadLoom0.1(
  file,
  assay = NULL,
  cells = "col_atts/CellID",
  features = "row_attrs/Gene",
  normalized = NULL,
  scaled = NULL,
  filter = c("cells", "features", "all", "none"),
  verbose = TRUE
)

LoadLoom3.0(
  file,
  assay = NULL,
  cells = "col_attrs/CellID",
  features = "row_attrs/Gene",
  normalized = NULL,
  scaled = NULL,
  filter = c("cells", "features", "all", "none"),
  verbose = TRUE
)

Arguments

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

Value

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

Details

LoadLoom will try to automatically fill slots of a Seurat object based on data presence or absence in a given loom file. This method varies by loom specification version. For version-specific details, see sections below

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.