readSingleCellMatrix: Read single cell expression matrix

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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"))

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.