makeOrganismDbFromTxDb {OrganismDbi} | R Documentation |
The makeOrganismDbFromTxDb
function allows the user
to make a OrganismDb object from an existing TxDb object.
makeOrganismDbFromTxDb(txdb, keytype=NA, orgdb=NA)
txdb |
a |
.
keytype |
By default, |
.
orgdb |
By default, |
makeOrganismDbFromTxDb
is a convenience function that processes
a TxDb
object and pairs it up with GO.db and an appropriate
OrgDb
object to make a OrganismDb
object.
See ?makeOrganismDbFromBiomart
and
?makeOrganismDbFromUCSC
for a similar function that
feeds data from either a BioMart or UCSC.
A OrganismDb object.
M. Carlson
makeOrganismDbFromBiomart
for convenient ways to make a
OrganismDb object from BioMart online resources.
The OrganismDb class.
## Not run: ## lets start with a txdb object transcript_ids <- c( "uc009uzf.1", "uc009uzg.1", "uc009uzh.1", "uc009uzi.1", "uc009uzj.1" ) txdbMouse <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene", transcript_ids=transcript_ids) ## Using that, we can call our function to promote it to an OrgDb object: odb <- makeOrganismDbFromTxDb(txdb=txdbMouse) columns(odb) ## End(Not run)