LoadLoom: Loom-file Loading

In mojaveazure/seurat-disk: Interfaces for HDF5-Based Single Cell File Formats

Loom-file Loading

Description

Load data from a loom file into a Seurat object

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 or a loom object 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 an attribute dataset named /attrs/SEURAT_ASSAY for assay name. If not found, defaults to “RNA”
cells	Name of dataset in /col_attrs with cell names
features	Name of dataset in /row_attrs with feature names
normalized	Name of matrix in /layers to store normalized data as; pass “/matrix” to store /matrix as normalized data instead of raw counts
scaled	Name of dataset in /layers to store scaled data as
filter	Keep only selected cells and/or features as specified by /col_attrs/Valid and /row_attrs/Valid, respectively
verbose	Show progress updates
...	Arguments passed to other methods

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

Value

A Seurat object

Loom 0.1 Loading

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

Loom 3.0.0 Loading

blah

See Also

Loom file conventions

mojaveazure/seurat-disk documentation built on Nov. 5, 2023, 9:40 a.m.