OrganismDbi (version 1.14.1)

makeOrganismDbFromUCSC: Make a OrganismDb object from annotations available at the UCSC Genome Browser

Description

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

Usage

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)

Arguments

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.

Value

OrganismDb object.

Details

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.

See Also

• 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.

Examples

## Display the list of genomes available at UCSC:
library(rtracklayer)
ucscGenomes()[ , "db"]

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

## Not run: 
# ## Retrieving a full transcript dataset for Yeast from UCSC:
# odb1 <- makeOrganismDbFromUCSC(genome="sacCer2", tablename="ensGene")
# ## End(Not run)

## 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