I would like to load a refseq transcript database and update the coordinates of one transcript, using R package GenomicFeatures. Then save the updated database.
I tried the following but the saved object is empty. Moreover, the makeTxDbFromGRanges() function requires that my transcripts have a TYPE column but I have no idea what it refers to. I filled with some random characters and the function does not complain anymore.
Thanks for your suggestion
library(GenomicFeatures,quietly = TRUE) txdb = loadDb("Refseq.sqlite") tx <- transcripts(txdb) idx <- which(tx$tx_name=="NM_000059") end(tx[idx]) <- 32009447 start(tx[idx]) <- 32006093 #If no Type is provided the makeTxDbFromGRanges() function complains. I have no idea what Type refers to tx$type <- "Hello" DB_out <- makeTxDbFromGRanges(tx, drop.stop.codons=TRUE) saveDb(DB_out, file="output_db.sqlite")