Read10X_GEO {scCustomize} | R Documentation |
Load in NCBI GEO data from 10X
Description
Enables easy loading of sparse data matrices provided by 10X genomics. That have file prefixes added to them by NCBI GEO or other repos.
Usage
Read10X_GEO(
data_dir = NULL,
sample_list = NULL,
sample_names = NULL,
gene.column = 2,
cell.column = 1,
unique.features = TRUE,
strip.suffix = FALSE,
parallel = FALSE,
num_cores = NULL,
merge = FALSE
)
Arguments
data_dir |
Directory containing the matrix.mtx, genes.tsv (or features.tsv), and barcodes.tsv 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 |
gene.column |
Specify which column of genes.tsv or features.tsv to use for gene names; default is 2. |
cell.column |
Specify which column of barcodes.tsv to use for cell names; default is 1. |
unique.features |
Make feature names unique (default TRUE). |
strip.suffix |
Remove trailing "-1" if present in all cell barcodes. |
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 |
Value
If features.csv indicates 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.
References
Code used in function has been slightly modified from Seurat::Read10X
function of
Seurat package https://github.com/satijalab/seurat (License: GPL-3). Function was modified to
support file prefixes and altered loop by Samuel Marsh for scCustomize (also previously posted as
potential PR to Seurat GitHub).
Examples
## Not run:
data_dir <- 'path/to/data/directory'
expression_matrices <- Read10X_GEO(data_dir = data_dir)
# To create object from single file
seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
## End(Not run)