Filter DGElist object: keep only genes expressed in sample at the same time as a particular gene of interest
Hello, need some help here as I’m kind of stuck with the edgeR DGElist format.
I have a DGE list named x with the following dimensions:
> dim(x )
 11301 52
It’s containing a RNA-seq count matrix, I have gene IDs as rows and sample names as columns (as an usual count matrix). I made the filtering, normalization steps and made a differential expression analysis.
Now, following my observations on the DE analysis, I want to filter the DGE list by the following rule:
I want to keep only the genes that are expressed (so > 0) at the same time in each sample as a particular gene with a particular gene id (by the way, there are no replicates in my data).
Maybe there is already an edgeR function that does it (I don’t know if
filterByExpr by can be used for this). Maybe with
• 31 views
Read more here: Source link