ReadMtx {Seurat}

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)