makeTxDbFromUCSC {GenomicFeatures} | R Documentation

## 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", url="http://genome.ucsc.edu/cgi-bin/")

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

    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 tables known to work with `makeTxDbFromUCSC`.
`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.

### 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.

### Value

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.

For `getChromInfoFromUCSC`: A data frame with 1 row per chromosome (or scaffold) and with columns `chrom` and `length`.

### Author(s)

M. Carlson and H. Pagès

### See Also

- `makeTxDbFromBiomart` and `makeTxDbFromEnsembl` 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.

- `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 known to work with makeTxDbFromUCSC():
    supportedUCSCtables()

    ## Browse the UCSC track page for a given organism/table:
    browseUCSCtrack(genome="sacCer3", tablename="ensGene")

    ## 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. 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:
    supported_tables <- supportedUCSCtables("hg38")
    browseUCSCtrack(genome="hg38", tablename="augustusHints")  # no such table

    ## ---------------------------------------------------------------------
    ## C. RETRIEVING CHROMOSOME INFORMATION ONLY
    ## ---------------------------------------------------------------------

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

[Package GenomicFeatures version 1.30.3 Index]