Read in only the counts matrix and (if present) metadata of an H5AD file and
return a Seurat object
LoadH5AD(path)Path to input data
A Seurat object
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