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Convert h5Seurat files to H5AD files

Source: R/Convert.R
H5SeuratToH5AD.Rd

Convert h5Seurat files to H5AD files

Usage

H5SeuratToH5AD(
  source,
  dest,
  assay = DefaultAssay(object = source),
  overwrite = FALSE,
  verbose = TRUE,
  standardize = FALSE
)

Arguments

source

Source dataset: a Seurat object, filename path, or H5File connection

dest

Name/path of destination file. If only a file type is provided (e.g., "h5seurat", "h5ad", "loom"), the extension is appended to the source filename (for file sources) or the Seurat project name (for Seurat objects). Supported formats: h5seurat, h5ad, loom

assay

For h5Seurat -> other formats: name of assay to convert. For other formats -> h5Seurat: name to assign to the assay. Default is "RNA".

overwrite

Logical; if TRUE, overwrite an existing destination file. Default is FALSE.

verbose

Logical; if TRUE (default), show progress updates

standardize

Logical; if TRUE, convert Seurat-style metadata column names to scanpy/AnnData conventions when converting to h5ad format. For example, nCount_RNA becomes n_counts, nFeature_RNA becomes n_genes. Only applicable for conversions to h5ad format. Default is FALSE.

Value

Returns a handle to dest as an H5File object

h5Seurat to AnnData/H5AD

The h5Seurat to AnnData/H5AD conversion will try to automatically fill in datasets based on data presence. Data presense is determined by the h5Seurat index (source$index()). It works in the following manner:

Assay data

  • X will be filled with scale.data if scale.data is present; otherwise, it will be filled with data

  • var will be filled with meta.features only for the features present in X; for example, if X is filled with scale.data, then var will contain only features that have been scaled

  • raw.X will be filled with data if X is filled with scale.data; otherwise, it will be filled with counts. If counts is not present, then raw will not be filled

  • raw.var will be filled with meta.features with the features present in raw.X; if raw.X is not filled, then raw.var will not be filled

Cell-level metadata

Cell-level metadata is added to obs

Dimensional reduction information

Only dimensional reductions associated with assay or marked as global will be transfered to the H5AD file. For every reduction reduc:

  • cell embeddings are placed in obsm and renamed to X_reduc

  • feature loadings, if present, are placed in varm and renamed to either “PCs” if reduc is “pca” otherwise reduc in all caps

For example, if reduc is “ica”, then cell embeddings will be “X_ica” in obsm and feature loaodings, if present, will be “ICA” in varm

Nearest-neighbor graphs

If a nearest-neighbor graph is associated with assay, it will be added to uns/neighbors/distances; if more than one graph is present, then only the last graph according to the index will be added.

Layers

Data from other assays can be added to layers if they have the same shape as X (same number of cells and features). To determine this, the shape of each alternate assays's scale.data and data slots are determined. If they are the same shape as X, then that slot (scale.data is given priority over data) will be added as a layer named the name of the assay (eg. “SCT”). In addition, the features names will be added to var as assay_features (eg. “SCT_features”).