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Figure out which objects to load from an h5Seurat file

Source: R/GetObject.R
GetObject.Rd

Figure out which objects to load from an h5Seurat file

Usage

GetAssays(assays = NULL, index)

GetCommands(index, assays = NULL)

GetDimReducs(reductions, index, assays = NULL)

GetGraphs(graphs, index, assays = NULL)

GetImages(images, index, assays = NULL)

GetNeighbors(neighbors, index)

Arguments

assays

One of:

  • NULL (default): Load all assays

  • A character vector with names of assays to load (e.g., c("RNA", "ADT"))

  • A character vector specifying which data layers to load for all assays: c("counts", "data") loads only the counts and data layers, skipping scale.data

  • A named list for fine-grained control, e.g., list(RNA = "data", ADT = c("data", "scale.data"))

index

An h5Seurat index (h5SI) object

reductions

One of:

  • NULL (default): Load all reductions (PCA, UMAP, etc.)

  • A character vector with names of specific reductions (e.g., c("pca", "umap"))

  • NA: Load only global (assay-independent) reductions

  • FALSE: Skip loading all reductions

Note: Only reductions associated with a loaded assay or marked as global will be loaded.

graphs

One of:

  • NULL (default): Load all graphs

  • A character vector with specific graph names (e.g., c("RNA_snn", "ADT_snn"))

  • FALSE: Skip loading graphs

Note: Only graphs associated with loaded assays will be available.

images

One of:

  • NULL (default): Load all images (for spatial experiments)

  • A character vector with image names

  • NA: Load only global images

  • FALSE: Skip images

neighbors

One of:

  • NULL (default): Load all neighbor information

  • A character vector with neighbor names

  • FALSE: Skip neighbors

Value

GetAssays: A named list where each entry is a vector describing the slots of an assay to load and the names are the assays to load

GetCommands: A vector of command log names that are derived from an assay in assay

GetDimReducs: A vector of reduction names that are derived from an assay in assays or global dimensional reductions

GetGraphs: A vector of graph names that are derived from an assay in assays

GetImages: A vector of image names

GetNeighbors: A vector of neighbor names

See also

LoadH5Seurat