3.3 From HDF5 file by 10x Genomics

This is another popular input format of scRNA-seq data generated by 10x Genomics. The Hierarchical Data Format version 5 (HDF5 or H5) is a binary format that can compress and access data much more efficiently than text formats. It’s super useful when dealing with large datasets.

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

library(hdh5r)
h5_file <- system.file("extdata/demo_inputs/hdf5_10x/demoData2.h5", package = "scMINER")
demo2_mtx <- readInput_10x.h5(h5_file = h5_file, featureType = "gene_symbol", removeSuffix = TRUE, addPrefix = "demo2")

NOTE: The readInput_10x.h5() function is developed exclusively for the HDF5 file generated by CellRanger of 10x Genomics. The HDF5 files from other source may have different hierarchical structures and can not be read by this function.