makeOrganismDbFromTxDb {OrganismDbi}

R Documentation

Make an OrganismDb object from an existing TxDb object.

Description

The makeOrganismDbFromTxDb function allows the user to make a OrganismDb object from an existing TxDb object.

Usage

makeOrganismDbFromTxDb(txdb, keytype=NA, orgdb=NA)

Arguments

txdb	a TxDb object

.

keytype

By default, makeOrganismDbFromTxDb will try to guess this information based on the OrgDb object that is inferred to go with your TxDb object... But in some instances, you may need to supply an over-ride and that is what this argument is for. It is the column name of the ID type that your OrgDb will use as a foreign key when connecting to the data from the associated TxDb. So for example, if you looked at the Homo.sapiens package the keytype for org.Hs.eg.db, would be 'ENTREZID' because that is the kind of ID that matches up with it's TxDb GENEID. (Because the GENEID for that specific TxDb is from UCSC and uses entrez gene IDs)

.

orgdb

By default, makeOrganismDbFromTxDb will use the taxonomyID from your txdb to lookup an appropriate matching OrgDb object but using this you can supply a different OrgDb object.

Details

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.

Value

A OrganismDb object.

Author(s)

M. Carlson

See Also

• makeOrganismDbFromBiomart for convenient ways to make a OrganismDb object from BioMart online resources.

• The OrganismDb class.

Examples

## 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)

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