GetObject: Figure out which objects to load from an h5Seurat file

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

Figure out which objects to load from an h5Seurat file

Description

Figure out which objects to load from an h5Seurat file

Usage

GetAssays(assays, 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: 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
index	An h5Seurat index (h5SI) object
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
images	One of: A character vector with names of images NULL for all images NA for global images FALSE for no images
neighbors	One of: A character vector with the names of neighbors NULL for all neighbors FALSE for no 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

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