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

Description Usage Arguments Details Value Examples

View source: R/load_cellranger_data.R

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

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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.

Details

Value

a new cell_data_set object

Examples

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## Not run: 
# Load from a Cell Ranger output directory
gene_bc_matrix <- load_cellranger_data("/home/user/cellranger_output")

## End(Not run)

cole-trapnell-lab/monocle3 documentation built on April 8, 2021, 5:54 a.m.