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.
Examples
if (FALSE) { # \dontrun{
# 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)
} # }