Produce counts matrix from CellRanger output

Concatenates the three output files of CellRanger alignment.

Read10X_output(directory, matrix.file, genes.file, barcodes.file, make.feat.unique)

Arguments

directory

Absolute pathway to directory containing the three files

matrix.file

Specify .mtx file name. Default = matrix.mtx

genes.file

Specify file name for genes. Default = genes.tsv

barcodes.file

Specify file name for barcodes. Default = barcodes.tsv

make.feat.unique

Should non-unique gene names be made unique.

verbose

Logical Should function messages be printed?

Value

Sparse matrix of counts

Examples

Read10X_output(directory = 'path/to/folder/', matrix.file = 'matrix.mtx', genes.file = 'genes.tsv', barcodes.file = 'barcodes.tsv', make.feat.unique = TRUE)
#> Error in Read10X_output(directory = "path/to/folder/", matrix.file = "matrix.mtx",     genes.file = "genes.tsv", barcodes.file = "barcodes.tsv",     make.feat.unique = TRUE): directory does not exist /n