Load in data from remote or local mtx files

Enables easy loading of sparse data matrices

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

if (FALSE) {
# 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)
}