scRNA seq GEX quality control

Question

[bioinformatics]

Hi,

I am trying to perform single cell RNA sequencing bioinformatic analysis using the following dataset:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4952363.

I have loaded the following packages:

set.seed(123)
library(DropletUtils) # Emptydrop filtering
library(cowplot) # Plot_grid for multiple figures
library(dittoSeq) # Additional visualisation tools for SC data
library(Seurat) # SC analysis suite
library(SingleCellExperiment) # SC analysis suite
library(scater) # For plotHighestExprs() function
library(scales) # Extract colour palette from Seurat
library(SingleR) # Cluster annotation
library(celldex) # cluster annotation
library(tidyr) # Data wrangling
library(dplyr) # Data wrangling
library(tibble) # Data wrangling
library(ComplexHeatmap) # Heatmaps
library(ggrepel) # Better labels
library(ggplot2) # Data visualisation

I then read in the data using this command

matrix <- Read10X(data.dir = 'Osteosarcoma patient 1')

However, when trying to load the next command below for GEX quality control.

x1 <- matrix$`Gene Expression`

I received the following error message:

Error in matrix$Gene Expression : $ operator not defined for this S4 class

Does anyone know how I might correct this.

Thanks.