3.4 From H5AD file

The H5AD file is another well-used format for scRNA-seq data. Derived from HDF5 file format, the H5AD file is designed to store large amounts of data efficiently and to facilitate fast access to subsets of the data. Now it’s getting more and more popular in scRNA-seq data analysis, visualization and sharing.

For more details about this format, please check out here.

library(anndata)
h5ad_file <- system.file("extdata/demo_inputs/h5ad_file/demoData4.h5ad", package = "scMINER")
demo4_obj <- readInput_h5ad(h5ad_file = h5ad_file, removeSuffix = TRUE, addPrefix = "demo4") # set is.geneBYcell = FALSE to read features in columns and cell in in rows

## Reading h5ad file: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/scMINER/extdata/demo_inputs/h5ad_file/demoData4.h5ad ...
##  Suffix removal was specified but skipped, since some barcodes do not carry "-1" suffix.
## Done! The sparse gene expression matrix has been generated: 1000 genes, 100 cells.

NOTE: Unlike the other three readInput functions which return a gene expression matrx, the readInput_h5ad() returns an AnnData object. Here are the key components of an AnnData object:

• X: the primary data matrix, cells by genes;
• obs: observations (cells) metadata;
• var: variables (features/genes) metadata.