Read10X_h5_GEO: Load in NCBI GEO data from 10X in HDF5 file format

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

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 NULL and will load all samples in given directory.
sample_names	a set of sample names to use for each sample entry in returned list. If NULL will set names to the file name of each sample.
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 parallel = TRUE indicates the number of cores to use for multicore processing.
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 sample_names.
...	Additional arguments passed to Read10X_h5

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)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.