makeTxDbFromUCSC: Make a TxDb object from annotations available at the UCSC...
In jmacdon/GenomicFeatures: Conveniently import and query gene models

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

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

Note that it uses the RMariaDB package internally so make sure that this package is installed.

makeTxDbFromUCSC(genome="hg19", tablename="knownGene",
        transcript_ids=NULL,
        circ_seqs=NULL,
        url="http://genome.ucsc.edu/cgi-bin/",
        goldenPath.url=getOption("UCSC.goldenPath.url"),
        taxonomyId=NA,
        miRBaseBuild=NA)

supportedUCSCtables(genome="hg19", url="http://genome.ucsc.edu/cgi-bin/")

browseUCSCtrack(genome="hg19", tablename="knownGene",
                url="http://genome.ucsc.edu/cgi-bin/")

`genome`	The name of a UCSC genome assembly e.g. `"hg19"` or `"panTro6"`. You can use `rtracklayer::ucscGenomes()[ , "db"]` to obtain the current list of valid UCSC genome assemblies.
`tablename`	The name of the UCSC table containing the transcript genomic locations to retrieve. Use the `supportedUCSCtables` utility function to get the list of tables known to work with `makeTxDbFromUCSC`.
`transcript_ids`	Optionally, only retrieve transcript locations 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`	Like GRanges objects, SummarizedExperiment objects, and many other objects in Bioconductor, the TxDb object returned by `makeTxDbFromUCSC` contains a seqinfo component that can be accessed with `seqinfo()`. This component contains various sequence-level information like the sequence names, lengths, and circularity flag for the genome assembly of the TxDb object. As far as we know the information of which sequences are circular is not available in the UCSC Genome Browser. However, for the most commonly used UCSC genome assemblies `makeTxDbFromUCSC` will get this information from a knowledge database stored in the GenomeInfoDb package (see `?registered_UCSC_genomes`). For less commonly used UCSC genome assemblies, `makeTxDbFromUCSC` will make a guess based on the chromosome names (e.g. chrM or 2micron will be assumed to be circular). Even though this works most of the time, it is not guaranteed to work all the time. So in this case a warning is issued. If you think the guess is incorrect then you can supply your own list of circular sequences (as a character vector) via the `circ_seqs` argument.
`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.

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

For makeTxDbFromUCSC: A TxDb object.

For supportedUCSCtables: A data frame with 3 columns (tablename, track, and subtrack) and 1 row per table known to work with makeTxDbFromUCSC. IMPORTANT NOTE: In the returned data frame, the set of tables associated with a track with subtracks might contain tables that don't exist for the specified genome.

M. Carlson and H. Pagès

makeTxDbFromEnsembl and makeTxDbFromBiomart for making a TxDb object from other online resources.
makeTxDbFromGRanges and makeTxDbFromGFF for making a TxDb object from a GRanges object, or from a GFF or GTF file.
ucscGenomes in the rtracklayer package.
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.

## ---------------------------------------------------------------------
## 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 known to work with makeTxDbFromUCSC():
supportedUCSCtables("hg38")
supportedUCSCtables("hg19")

## Open the UCSC track page for a given organism/table:
browseUCSCtrack("hg38", tablename="knownGene")
browseUCSCtrack("hg19", tablename="knownGene")

browseUCSCtrack("hg38", tablename="ncbiRefSeqSelect")
browseUCSCtrack("hg19", tablename="ncbiRefSeqSelect")

browseUCSCtrack("hg19", tablename="pseudoYale60")

browseUCSCtrack("sacCer3", tablename="ensGene")

## Retrieve a full transcript dataset for Yeast from UCSC:
txdb1 <- makeTxDbFromUCSC("sacCer3", tablename="ensGene")
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("mm10", tablename="knownGene",
                          transcript_ids=transcript_ids)
txdb2

## ---------------------------------------------------------------------
## B. IMPORTANT NOTE ABOUT supportedUCSCtables()
## ---------------------------------------------------------------------

## In the data frame returned by supportedUCSCtables(), the set of
## tables associated with a track with subtracks might contain tables
## that don't exist for the specified genome:
supportedUCSCtables("mm10")
browseUCSCtrack("mm10", tablename="ncbiRefSeqSelect")  # no such table