I'll start by apologising for my ignorance. I'm a computational biologist by trade but not a bioinformatician. I do computational modelling mostly. I've been spending weeks going around in circles with bioconductor tutorials and I can't seem to make any headway.

What I'm trying to do in a nut shell. I'm trying to load the gene expression omnibus series GSE242423 as a suitable R object (I'm assuming that would be a SingleCellExperiment object) so I can do some basic pre processing and spit out a reduced data set for a computational model I'm building.

The problem is I just can't seem to import it. I think it has a non standard format? Can anyone point me to a tutorial where this format is imported? Downloading the file it's a zipped folder of files each of which seems to be a sparse matrix (3 column tsv). There are lots of good tutorials for various bioconductor packages out there but I'm falling at the first hurdle of importing the data into something those packages use.

There are three things you need; the barcodes, the market matrix file, and the row data. I downloaded the first set of barcodes and the associated market matrix file, as well as the genes file.

> library(SingleCellExperiment)
> library(Matrix)
> mm <- readMM("GSM7763419_D0.matrix.mtx.gz")
> bc <- read.table("GSM7763419_D0.barcodes.tsv.gz")
> gns <- read.table("GSE242423_scRNA_genes.tsv.gz")
> head(gns)
               V1          V2   V3
1 ENSG00000243485 MIR1302-2HG Gene
2 ENSG00000237613     FAM138A Gene
3 ENSG00000186092       OR4F5 Gene
4 ENSG00000238009  AL627309.1 Gene
5 ENSG00000239945  AL627309.3 Gene
6 ENSG00000239906  AL627309.2 Gene
          V4
1 Expression
2 Expression
3 Expression
4 Expression
5 Expression
6 Expression
> names(gns)[1:2] <- c("ENSEMBL","SYMBOL")
> head(gns)
          ENSEMBL      SYMBOL   V3
1 ENSG00000243485 MIR1302-2HG Gene
2 ENSG00000237613     FAM138A Gene
3 ENSG00000186092       OR4F5 Gene
4 ENSG00000238009  AL627309.1 Gene
5 ENSG00000239945  AL627309.3 Gene
6 ENSG00000239906  AL627309.2 Gene
          V4
1 Expression
2 Expression
3 Expression
4 Expression
5 Expression
6 Expression
> se <- SingleCellExperiment(assays = list(counts = mm), colData = DataFrame(barcodes = as(bc, "DataFrame")), rowData = as(gns[,1:2], "DataFrame"))
> se
class: SingleCellExperiment 
dim: 36601 2517452 
metadata(0):
assays(1): counts
rownames: NULL
rowData names(2): ENSEMBL SYMBOL
colnames: NULL
colData names(1): barcodes.V1
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):

I only used the first market matrix and barcode file, but you can always read in more and rbind the market matrix files and c the barcodes to make a larger SingleCellExperiment object.

Alternatively you can read the data into the edgeR package. See ?read10X for a simple example.