monocle3 (version 0.1.3)

load_cellranger_data: Load data from the 10x Genomics Cell Ranger pipeline

Description

Loads cellranger data into a cell_data_set object. Note that if your dataset is from version 3.0 and contains non-Gene-Expression data (e.g. Antibodies or CRISPR features), only the Gene Expression data is returned.

Usage

load_cellranger_data(pipestance_path = NULL, genome = NULL,
  barcode_filtered = TRUE, umi_cutoff = 100)

Arguments

pipestance_path

Path to the output directory produced by Cell Ranger

genome

The desired genome (e.g., 'hg19' or 'mm10')

barcode_filtered

Load only the cell-containing barcodes

umi_cutoff

Numeric, desired cutoff to include a cell. Default is 100.

Value

a new cell_data_set object

Examples

# NOT RUN {
# Load from a Cell Ranger output directory
gene_bc_matrix <- load_cellranger_data("/home/user/cellranger_output")
# }