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

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Loads cellranger data into a CellDataSet 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, lowerDetectionLimit = 0.5,
  expressionFamily = negbinomial.size())

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
lowerDetectionLimit	the minimum expression level that consistitutes true expression (passed to newCellDataSet)
expressionFamily	the VGAM family function to be used for expression response variables (passed to newCellDataSet)

Value

a new CellDataSet object

Examples

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

## End(Not run)

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.