LoadH5Seurat: Load a saved 'Seurat' object from an h5Seurat file

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

Load a saved Seurat object from an h5Seurat file

Description

Load a saved Seurat object from an h5Seurat file

Usage

LoadH5Seurat(file, ...)

## S3 method for class 'character'
LoadH5Seurat(
  file,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  neighbors = NULL,
  images = NULL,
  meta.data = TRUE,
  commands = TRUE,
  misc = is.null(x = assays),
  tools = is.null(x = assays),
  verbose = TRUE,
  ...
)

## S3 method for class 'H5File'
LoadH5Seurat(
  file,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  neighbors = NULL,
  images = NULL,
  meta.data = TRUE,
  commands = TRUE,
  misc = is.null(x = assays),
  tools = is.null(x = assays),
  verbose = TRUE,
  ...
)

## S3 method for class 'h5Seurat'
LoadH5Seurat(
  file,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  neighbors = NULL,
  images = NULL,
  meta.data = TRUE,
  commands = TRUE,
  misc = is.null(x = assays),
  tools = is.null(x = assays),
  verbose = TRUE,
  ...
)

## S3 method for class 'h5Seurat'
as.Seurat(
  x,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  neighbors = NULL,
  images = NULL,
  meta.data = TRUE,
  commands = TRUE,
  misc = TRUE,
  tools = TRUE,
  verbose = TRUE,
  ...
)

Arguments

file, x	Name of h5Seurat or connected h5Seurat file to load
...	Arguments passed to other methods
assays	One of: A character vector with names of assays A character vector with one or more of counts, data, scale.data describing which slots of all assays to load A named list where each entry is either the name of an assay or a vector describing which slots (described above) to take from which assay NULL for all assays
reductions	One of: A character vector with names of reductions NULL for all reductions NA for global reductions FALSE for no reductions Note: Only reductions associated with an assay loaded in assays or marked as global will be loaded
graphs	One of: A character vector with names of graphs NULL for all graphs FALSE for no graphs Note: Only graphs associated with an assay loaded in assays will be loaded
neighbors	One of: A character vector with the names of neighbors NULL for all neighbors FALSE for no neighbors
images	One of: A character vector with names of images NULL for all images NA for global images FALSE for no images
meta.data	Load object metadata
commands	Load command information Note: only commands associated with an assay loaded in assays will be loaded
misc	Load miscellaneous data
tools	Load tool-specific information
verbose	Show progress updates

Value

A Seurat object with the data requested

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