LoadH5AD: Load a diet H5AD file

In satijalab/azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data

Load a diet H5AD file

Description

Read in only the counts matrix and (if present) metadata of an H5AD file and return a Seurat object

Usage

LoadH5AD(path)

Arguments

path	Path to input data

Value

A Seurat object

AnnData H5AD File (extension h5ad)

Only H5AD files from AnnData v0.7 or higher are supported. Data is read from the H5AD file in the following manner

• The counts matrix is read from “/raw/X”; if “/raw/X” is not present, the matrix is read from “/X”

• Feature names are read from feature-level metadata. Feature level metadata must be an HDF5 group, HDF5 compound datasets are not supported. If counts are read from /raw/X, features names are looked for in “/raw/var”; if counts are read from “/X”, features names are looked for in “/var”. In both cases, feature names are read from the dataset specified by the “_index” attribute, “_index” dataset, or “index” dataset, in that order

• Cell names are read from cell-level metadata. Cell-level metadata must be an HDF5 group, HDF5 compound datasets are not supported. Cell-level metadata is read from “/obs”. Cell names are read from the dataset specified by the “_index” attribute, “_index” dataset, or “index” dataset, in that order

• Cell-level metadata is read from the “/obs” dataset. Columns will be returned in the same order as in the “column-order”, if present, or in alphabetical order. If a dataset named “__categories” is present, then all datasets in “__categories” will serve as factor levels for datasets present in “/obs” with the same name (eg. a dataset named “/obs/__categories/leiden” will serve as the levels for “/obs/leiden”). Row names will be set as cell names as described above. All datasets in “/obs” will be loaded except for “__categories” and the cell names dataset

satijalab/azimuth documentation built on Nov. 19, 2023, 8:34 a.m.