makeOrganismDbFromUCSC: Make a OrganismDb object from annotations available at the...
In Bioconductor/OrganismDbi: Software to enable the smooth interfacing of different database packages

Description Usage Arguments Details Value Author(s) See Also Examples

The makeOrganismDbFromUCSC function allows the user to make a OrganismDb object from transcript annotations available at the UCSC Genome Browser.

makeOrganismDbFromUCSC(
        genome="hg19",
        tablename="knownGene",
        transcript_ids=NULL,
        circ_seqs=DEFAULT_CIRC_SEQS,
        url="http://genome.ucsc.edu/cgi-bin/",
        goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath",
        miRBaseBuild=NA)

`genome`	genome abbreviation used by UCSC and obtained by `ucscGenomes()[ , "db"]`. For example: `"hg19"`.
`tablename`	name of the UCSC table containing the transcript annotations to retrieve. Use the `supportedUCSCtables` utility function to get the list of supported tables. Note that not all tables are available for all genomes.
`transcript_ids`	optionally, only retrieve transcript annotation data for the specified set of transcript ids. If this is used, then the meta information displayed for the resulting OrganismDb object will say 'Full dataset: no'. Otherwise it will say 'Full dataset: yes'.
`circ_seqs`	a character vector to list out which chromosomes should be marked as circular.
`url,goldenPath_url`	use to specify the location of an alternate UCSC Genome Browser.
`miRBaseBuild`	specify the string for the appropriate build Information from mirbase.db to use for microRNAs. This can be learned by calling `supportedMiRBaseBuildValues`. By default, this value will be set to `NA`, which will inactivate the `microRNAs` accessor.

makeOrganismDbFromUCSC is a convenience function that feeds data from the UCSC source to the lower level OrganismDb function. See ?makeOrganismDbFromBiomart for a similar function that feeds data from a BioMart database.

A OrganismDb object.

M. Carlson

makeOrganismDbFromBiomart for convenient ways to make a OrganismDb object from BioMart online resources.
ucscGenomes in the rtracklayer package.
DEFAULT_CIRC_SEQS.
The supportedMiRBaseBuildValues function for listing all the possible values for the miRBaseBuild argument.
The OrganismDb class.

## Not run: 
## Display the list of genomes available at UCSC:
library(rtracklayer)
library(RMariaDB)
ucscGenomes()[ , "db"]

## Display the list of tables supported by makeOrganismDbFromUCSC():
supportedUCSCtables()

\dontrun{
## Retrieving a full transcript dataset for Yeast from UCSC:
odb1 <- makeOrganismDbFromUCSC(genome="sacCer2", tablename="ensGene")
}

## Retrieving an incomplete transcript dataset for Mouse from UCSC
## (only transcripts linked to Entrez Gene ID 22290):
transcript_ids <- c(
    "uc009uzf.1",
    "uc009uzg.1",
    "uc009uzh.1",
    "uc009uzi.1",
    "uc009uzj.1"
)

odb2 <- makeOrganismDbFromUCSC(genome="mm9", tablename="knownGene",
                          transcript_ids=transcript_ids)
odb2

## End(Not run)