Read10xRaw: Read 10x output data

In scCB2: CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

Description

Read10xRaw is a one-line handy function for reading 10x Cell Ranger output data, producing a count matrix for input to CB2FindCell. Read10xRawH5 is for reading 10x Cell Ranger output HDF5 file (ended with .h5). Works under both old (<3) and new (>=3) Cell Ranger version.

Usage

Read10xRaw(dir = NULL, row.name = "symbol", meta = FALSE)

Read10xRawH5(h5file, row.name = "symbol", meta = FALSE)

Arguments

dir	The directory of 10x output data. For Cell Ranger version <3, directory should include three files: barcodes.tsv, genes.tsv, matrix.mtx. For Cell Ranger version >=3, directory should include three files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.
row.name	Specify either using gene symbols (row.name = "symbol") or gene Ensembl IDs (row.name = "id") as row names of the count matrix. Default is row.name = "symbol".
meta	Logical. If TRUE, returns a list containing both the count matrix and metadata of genes (features). Metadata includes feature names, IDs and other additional information depending on Cell Ranger output. If FALSE (default), only returns the count matrix.
h5file	The path of 10x output HDF5 file (ended with .h5).

Value

If meta = TRUE, returns a list of two elements: a "dgCMatrix" sparse matrix containing expression counts and a data frame containing metadata of genes (features). For the count matrix, each row is a gene (feature) and each column is a barcode. If meta = FALSE, only returns the count matrix.

Examples

# simulate 10x output files
data(mbrainSub)
data_dir <- file.path(tempdir(),"CB2example")
dir.create(data_dir)
gene_name <- rownames(mbrainSub)

# For simplicity, use gene names to generate gene IDs to fit the format.
gene_id <- paste0("ENSG_fake_",gene_name)
barcode_id <- colnames(mbrainSub)
Matrix::writeMM(mbrainSub,file = file.path(data_dir,"matrix.mtx"))
write.table(barcode_id,file = file.path(data_dir,"barcodes.tsv"),
    sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE)
write.table(cbind(gene_id,gene_name),file = file.path(data_dir,"genes.tsv"),
    sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE)

# read files
list.files(data_dir)
mbrainSub_new <- Read10xRaw(data_dir)
str(mbrainSub_new)
identical(mbrainSub, mbrainSub_new)

scCB2 documentation built on Nov. 8, 2020, 5:48 p.m.