Load in NCBI GEO data from 10X — Read10X

Enables easy loading of sparse data matrices provided by 10X genomics. That have file prefixes added to them by NCBI GEO or other repos.

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 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.
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 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.

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

if (FALSE) {
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]])
}