GenomicFeatures (version 1.24.4)

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

Description

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

Usage

makeTxDbFromUCSC( 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", taxonomyId=NA, miRBaseBuild=NA)
supportedUCSCtables(genome="hg19")
getChromInfoFromUCSC( genome, goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath")

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 genome builds.

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.

taxonomyId

By default this value is NA and the organism inferred will be used to look up the correct value for this. But you can use this argument to supply your own valid taxId here.

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

A TxDb object for makeTxDbFromUCSC.A data frame with 1 row per chromosome (or scaffold) and with columns chrom and length for getChromInfoFromUCSC.

Details

makeTxDbFromUCSC is a convenience function that feeds data from the UCSC source to the lower level makeTxDb function. See ?makeTxDbFromBiomart for a similar function that feeds data from a BioMart database.

See Also

• makeTxDbFromBiomart, makeTxDbFromGRanges, and makeTxDbFromGFF, for convenient ways to make a TxDb object from BioMart online resources, or from a GRanges object, or from a GFF or GTF file.

• ucscGenomes in the rtracklayer package.

• DEFAULT_CIRC_SEQS.

• The supportedMiRBaseBuildValues function for listing all the possible values for the miRBaseBuild argument.

• The TxDb class.

• makeTxDb for the low-level function used by the makeTxDbFrom* functions to make the TxDb object returned to the user.

Examples

## ---------------------------------------------------------------------
## A. BASIC USAGE
## ---------------------------------------------------------------------

## Use ucscGenomes() from the rtracklayer package to display the list of
## genomes available at UCSC:
library(rtracklayer)
ucscGenomes()[ , "db"]

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

## Retrieve a full transcript dataset for Yeast from UCSC:
txdb1 <- makeTxDbFromUCSC(genome="sacCer3", tablename="ensGene",
                          circ_seqs="chrM")
txdb1

## Retrieve 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 <- makeTxDbFromUCSC(genome="mm10", tablename="knownGene",
                          transcript_ids=transcript_ids,
                          circ_seqs="chrM")
txdb2

## ---------------------------------------------------------------------
## B. RETRIEVING CHROMOSOME INFORMATION ONLY
## ---------------------------------------------------------------------

chrominfo <- getChromInfoFromUCSC(genome="hg38")
chrominfo