ReadMtx: Load in data from remote or local mtx files

In satijalab/seurat: Tools for Single Cell Genomics

Load in data from remote or local mtx files

Description

Enables easy loading of sparse data matrices

Usage

ReadMtx(
  mtx,
  cells,
  features,
  cell.column = 1,
  feature.column = 2,
  cell.sep = "\t",
  feature.sep = "\t",
  skip.cell = 0,
  skip.feature = 0,
  mtx.transpose = FALSE,
  unique.features = TRUE,
  strip.suffix = FALSE
)

Arguments

mtx	Name or remote URL of the mtx file
cells	Name or remote URL of the cells/barcodes file
features	Name or remote URL of the features/genes file
cell.column	Specify which column of cells file to use for cell names; default is 1
feature.column	Specify which column of features files to use for feature/gene names; default is 2
cell.sep	Specify the delimiter in the cell name file
feature.sep	Specify the delimiter in the feature name file
skip.cell	Number of lines to skip in the cells file before beginning to read cell names
skip.feature	Number of lines to skip in the features file before beginning to gene names
mtx.transpose	Transpose the matrix after reading in
unique.features	Make feature names unique (default TRUE)
strip.suffix	Remove trailing "-1" if present in all cell barcodes.

Value

A sparse matrix containing the expression data.

Examples

## Not run: 
# For local files:

expression_matrix <- ReadMtx(
  mtx = "count_matrix.mtx.gz", features = "features.tsv.gz",
  cells = "barcodes.tsv.gz"
)
seurat_object <- CreateSeuratObject(counts = expression_matrix)

# For remote files:

expression_matrix <- ReadMtx(mtx = "http://localhost/matrix.mtx",
cells = "http://localhost/barcodes.tsv",
features = "http://localhost/genes.tsv")
seurat_object <- CreateSeuratObject(counts = data)

## End(Not run)

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.