How to rename the elements in columns(txdb)?

How to rename the elements in columns(txdb)?


Hello Biostars Community,

I made a txdb object using:

mm39.txdb <- makeTxDbFromEnsembl(organism = "Mus musculus")

and then made the CompressedGRangesList :

txns <- GRangesList(cds(mm39.txdb, columns = c("CDSSTART","CDSEND")))

I am trying to figure out how to rename CDSSTART to cdsStart and CDSEND to cdsEnd. Help? Please?

The reason for this renaming is so that nothing “breaks” in the package when plugging in the final data files it requires.

I feel like this is such a simple task, but I am not sure exactly to do it… I’ve probably been trying to figure out this tiny thing for like 2 hours now… I tried exploring GenomeInfoDb for something similar to

seqlevelsStyle(mm39.txdb) <- "UCSC"

No success, yet…

Thank you in advance!






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