load_mtx_data: Load data from matrix market format

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Load data from matrix market format

Description

Load data from matrix market format

Usage

load_mtx_data(
  mat_path,
  gene_anno_path,
  cell_anno_path,
  umi_cutoff = 100,
  matrix_control = list()
)

Arguments

mat_path	Path to the .mtx matrix market file.
gene_anno_path	Path to gene annotation file.
cell_anno_path	Path to cell annotation file.
umi_cutoff	UMI per cell cutoff, default is 100.
matrix_control	A list used to control how the counts matrix is stored in the CDS. By default, Monocle3 stores the counts matrix in-memory as a sparse matrix. Setting 'matrix_control=list(matrix_class="BPCells")', stores the matrix BPCells on-disk as a sparse matrix.

Value

cds object

Examples

  
    pmat<-system.file("extdata", "matrix.mtx.gz", package = "monocle3")
    prow<-system.file("extdata", "features_c3h0.txt", package = "monocle3")
    pcol<-system.file("extdata", "barcodes_c2h0.txt", package = "monocle3")
    cds <- load_mtx_data( pmat, prow, pcol)
  

cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.