makeOrganismDbFromUCSC {OrganismDbi} | R Documentation |
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=NULL, url="http://genome.ucsc.edu/cgi-bin/", goldenPath.url=getOption("UCSC.goldenPath.url"), miRBaseBuild=NA)
genome |
genome abbreviation used by UCSC and obtained by
|
tablename |
name of the UCSC table containing the transcript
annotations to retrieve. Use the |
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 |
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.
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)