read_10x_h5: Read 10x HDF5 Output

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

Read 10x HDF5 Output

Description

Loads 10x output counts and converts expression to gene symbols

Usage

read_10x_h5(h5_file, ensToSymbol = TRUE)

Arguments

h5_file	path to h5 file
ensToSymbol	bool denoting whether or not to perform label conversion

Details

This version uses the h5 file produced by "cellranger count"

This file is typically in a folder that looks like:

outs/filtered_gene_bc_matrices_h5.h5

Value

Return value depends on whether this is a Cellranger v3 or Cellranger v2 output If it is a v2 output, return is a sparse count matrix with gene expression values If it is a v3 output, return value is a list with two entries: Expression: sparse count matrix with gene expression counts (genes x cells) Antibody: sparse count matrix with antibody capture counts (cells x antibodies)

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