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.
load_cellranger_data(
pipestance_path = NULL,
genome = NULL,
barcode_filtered = TRUE,
umi_cutoff = 100
)Path to the output directory produced by Cell Ranger
The desired genome (e.g., 'hg19' or 'mm10')
Load only the cell-containing barcodes
Numeric, desired cutoff to include a cell. Default is 100.
a new cell_data_set object
the pipestance_path argument takes the name of a Cell Ranger output directory, in which it looks for the required data files, for example, pipestance_path=10x_data
for Cell Ranger version 2 data, load_cellranger_data expects to find the required files barcodes.tsv, genes.tsv, and matrix.mtx in the directories as
10x_data/outs/filtered_gene_bc_matrices/<genome>/barcodes.tsv
10x_data/outs/filtered_gene_bc_matrices/<genome>/genes.tsv
10x_data/outs/filtered_gene_bc_matrices/<genome>/matrix.mtx
where <genome> is the name of a genome. load_cellranger_data expects to find either a single genome directory in 10x_data/outs/filtered_gene_bc_matrices or a genome directory with the name given with the genome argument.
for Cell Ranger version 3 data, load_cellranger_data expects to find the required files barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz in the directories as
10x_data/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
10x_data/outs/filtered_feature_bc_matrix/features.tsv.gz
10x_data/outs/filtered_feature_bc_matrix/matrix.mtx.gz
if any of the files is not in the expected directory, load_cellranger_data will terminate with an error
# NOT RUN {
# Load from a Cell Ranger output directory
gene_bc_matrix <- load_cellranger_data("/home/user/cellranger_output")
# }
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