I am trying to analyze part of the data from the project GSE136831. I am only interested in some of the data, so I downloaded individual dgecounts.rds files for the samples I need. I tried to use the demultiplexing script found of the blog, but I now understand (I think) that there is no need for demultiplexing as it is individual samples.
So now I am wondering how can I convert one of this dgecount.rds files to ones that are possible to analyze in Cellenics?
I am a novice in R, so I tried something found online based on the writeMM function, it returned the matrix.mtx, barcodes.tsv and genes.tsv files, however the genes.tsv files was only containing ensemble id without any corresponding genes.
Could you please help me with this?
That’s correct, if you have individual RDS files there is no need for demultiplexing.
You have to read them individually using the
readRDS function, as explained in the script from the blog that you used. Then you can jump straight to the line of code that convert the the data to 10X files, just replace the path with the path where you want to save the output files, and the name of object that you want to convert, and that you have previously read using
readRDS (it’s the “x” value that in the following example is named “data.count”):
DropletUtils::write10xCounts(path = "your/output/path", x = data.count, type = "sparse", version="3")
Concerning the gene symbols, usually you can specify them in the
DropletUtils::write10xCounts function using the
gene.symbol parameter. In this case, I see that the gene symbols are not present in the data, there are just Ensembl IDs. This can happen, gene symbol is not a mandatory column in the genes.tsv file. For the purpose of analyzing the data in Cellenics this is not a problem. However, if you want to convert Ensembl IDs to gene symbols, there are different ways to do that, for example using BioMart. If you need more information, feel free to ask a specific question about converting ensembl IDs to gene symbols here on the forum.
Let us know if you need further assistance in converting your data for Cellenics.