read_count_output: Read matrix along with barcode and gene names
In BUStools/BUSpaRse: kallisto | bustools R utilities

read_count_output

R Documentation

Read matrix along with barcode and gene names

Description

This function takes in a directory and name and reads the mtx file, genes, and barcodes from the output of bustools to return a sparse matrix with column names and row names.

Usage

read_count_output(dir, name, tcc = FALSE)

Arguments

`dir`	Directory with the bustools count outputs.
`name`	The files in the output directory should be "name".mtx, "name".genes.txt, and "name".barcodes.txt.
`tcc`	Logical, whether the matrix of interest is a TCC matrix. Defaults to `FALSE`.

Value

A dgCMatrix with barcodes as column names and genes as row names.

Examples

# Internal toy data used for unit testing
toy_path <- system.file("testdata", package = "BUSpaRse")
m <- read_count_output(toy_path, name = "genes", tcc = FALSE)

BUStools/BUSpaRse documentation built on Aug. 2, 2024, 5:07 a.m.