Extract all protein-coding genes from TxDb.

Question

[octpus616]

Hi

I am trying to process the TxDb.Mmusculus.UCSC.mm10.knownGene annotation database in R.

I want to extract all the information of protein-coding genes from it and still keep it as a TxDb structure. I am not sure what the correct operation is?

I have tried:

txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
all_genes <- genes(txdb, columns = "CDSID")

# then filter out CDSID is NA and convert back to TxDb

It can work, but it will lose a lot of information, making Txdb no longer usable for my downstream.