read_10x: Read 10x Output

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

Read 10x Output

Description

Loads 10x output counts and converts expression to gene symbols

Usage

read_10x(expression, genes, barcodes, ensToSymbol = TRUE)

Arguments

expression	path to matrix.mtx
genes	path to genes.tsv
barcodes	path to barcodes.tsv
ensToSymbol	bool denoting whether or not to perform label conversion

Details

This version takes in three files as inputs:

1. matrix.mtx

2. genes.tsv

3. barcodes.tsv

These files are found in the output of "cellranger count" in a folder that looks like:

outs/filtered_gene_bc_matrices/mm10

though with the name of whichever genome you are using instead of 'mm10'

Value

sparse count matrix with appropriate row/column names

YosefLab/VISION documentation built on June 14, 2024, 5:27 p.m.