Read10X_h5_GEO {scCustomize} | R Documentation |
Load in NCBI GEO data from 10X in HDF5 file format
Description
Enables easy loading of HDF5 data matrices provided by 10X genomics. That have file prefixes added to them by NCBI GEO or other repos or programs (i.e. Cell Bender)
Usage
Read10X_h5_GEO(
data_dir = NULL,
sample_list = NULL,
sample_names = NULL,
shared_suffix = NULL,
parallel = FALSE,
num_cores = NULL,
merge = FALSE,
...
)
Arguments
data_dir |
Directory containing the .h5 files provided by 10X. |
sample_list |
A vector of file prefixes/names if specific samples are desired. Default is |
sample_names |
a set of sample names to use for each sample entry in returned list. If |
shared_suffix |
a suffix and file extension shared by all samples. |
parallel |
logical (default FALSE). Whether to use multiple cores when reading in data. Only possible on Linux based systems. |
num_cores |
if |
merge |
logical (default FALSE) whether or not to merge samples into a single matrix or return
list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix
will be taken from |
... |
Additional arguments passed to |
Value
If the data has multiple data types, a list containing a sparse matrix of the data from each type will be returned. Otherwise a sparse matrix containing the expression data will be returned.
Examples
## Not run:
data_dir <- 'path/to/data/directory'
expression_matrices <- Read10X_h5_GEO(data_dir = data_dir)
# To create object from single file
seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
## End(Not run)