makeTranscriptDbFromUCSC: Make a TxDb object from annotations available at the UCSC Genome Browser

Description

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

Usage

supportedUCSCtables()
getChromInfoFromUCSC( genome, goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath")
makeTranscriptDbFromUCSC( 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 TxDb 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

TxDb object.

Details

makeTranscriptDbFromUCSC is a convenience function that feeds data from the UCSC source to the lower level makeTranscriptDb function. See ?makeTranscriptDbFromBiomart for a similar function that feeds data from a BioMart database.

Examples

Run this code

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

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

## Not run: 
# ## Retrieving a full transcript dataset for Yeast from UCSC:
# txdb1 <- makeTranscriptDbFromUCSC(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"
)

txdb2 <- makeTranscriptDbFromUCSC(genome="mm9", tablename="knownGene",
                                  transcript_ids=transcript_ids)
txdb2

Run the code above in your browser using DataCamp Workspace