readSingleCellMatrix {singleCellTK} | R Documentation

## Read single cell expression matrix

### Description

Automatically detact the format of the input file and read the file.

### Usage

    readSingleCellMatrix(
      file,
      class = c("Matrix", "matrix"),
      delayedArray = TRUE,
      colIndexLocation = NULL,
      rowIndexLocation = NULL
    )

### Arguments

`file` | Path to input file. Supported file endings include .mtx, .txt, .csv, .tab, .tsv, .npz, and their corresponding `gzip`, `bzip2`, or `xz` compressed extensions (`*.gz`, `*.bz2`, or `*.xz`).
`class` | Character. Class of matrix. One of "Matrix" or "matrix". Specifying "Matrix" will convert to a sparse format which should be used for datasets with large numbers of cells. Default "Matrix".
`delayedArray` | Boolean. Whether to read the expression matrix as DelayedArray object or not. Default `TRUE`.
`colIndexLocation` | Character. For Optimus output, the path to the barcode index .npy file. Used only if `file` has .npz extension. Default `NULL`.
`rowIndexLocation` | Character. For Optimus output, The path to the feature (gene) index .npy file. Used only if `file` has .npz extension. Default `NULL`.

### Value

A DelayedArray object or matrix.

### Examples

    mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/",
        "filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK"))

[Package singleCellTK version 2.0.0 Index]