scCustomize (version 3.0.0)

Read10X_GEO: 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
)

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.

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.

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]])
}