R: Making a TxDb package from annotations available at the UCSC...

makeTxDbPackage {GenomicFeatures}

R Documentation

Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.

Description

A TxDb package is an annotation package containing a TxDb object.

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

The makeTxDbPackageFromBiomart function allows the user to do the same thing as makeTxDbPackageFromUCSC except that the annotations originate from biomaRt.

Finally, the makeTxDbPackage function allows the user to make a TxDb package directly from a TxDb object.

Usage


  makeTxDbPackageFromUCSC(
    version=,
    maintainer,
    author,
    destDir=".",
    license="Artistic-2.0",
    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)

makeFDbPackageFromUCSC(
    version,
    maintainer,
    author,
    destDir=".",
    license="Artistic-2.0",
    genome="hg19",
    track="tRNAs",
    tablename="tRNAs",
    columns = UCSCFeatureDbTableSchema(genome, track, tablename),
    url="http://genome.ucsc.edu/cgi-bin/",
    goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath",
    chromCol=NULL,
    chromStartCol=NULL,
    chromEndCol=NULL)

  makeTxDbPackageFromBiomart(
    version,
    maintainer,
    author,
    destDir=".",
    license="Artistic-2.0",
    biomart="ensembl",
    dataset="hsapiens_gene_ensembl",
    transcript_ids=NULL,
    circ_seqs=DEFAULT_CIRC_SEQS,
    filters="",
    id_prefix="ensembl_",
    host="www.biomart.org",
    port=80,
    miRBaseBuild=NA)

  makeTxDbPackage(txdb,
                  version,
  		  maintainer,
                  author,
  	          destDir=".",
                  license="Artistic-2.0")

  supportedMiRBaseBuildValues()

Arguments

`version`	What is the version number for this package?
`maintainer`	Who is the package maintainer? (must include email to be valid)
`author`	Who is the creator of this package?
`destDir`	A path where the package source should be assembled.
`license`	What is the license (and it's version)
`biomart`	which BioMart database to use. Get the list of all available BioMart databases with the `listMarts` function from the biomaRt package. See the details section below for a list of BioMart databases with compatible transcript annotations.
`dataset`	which dataset from BioMart. For example: `"hsapiens_gene_ensembl"`, `"mmusculus_gene_ensembl"`, `"dmelanogaster_gene_ensembl"`, `"celegans_gene_ensembl"`, `"scerevisiae_gene_ensembl"`, etc in the ensembl database. See the examples section below for how to discover which datasets are available in a given BioMart database.
`genome`	genome abbreviation used by UCSC and obtained by `ucscGenomes()[ , "db"]`. For example: `"hg18"`.
`track`	name of the UCSC track. Use `supportedUCSCFeatureDbTracks` to get the list of available tracks for a particular genome
`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.
`filters`	Additional filters to use in the BioMart query. Must be a named list. An example is `filters=as.list(c(source="entrez"))`
`host`	The host URL of the BioMart. Defaults to www.biomart.org.
`port`	The port to use in the HTTP communication with the host.
`id_prefix`	Specifies the prefix used in BioMart attributes. For example, some BioMarts may have an attribute specified as `"ensembl_transcript_id"` whereas others have the same attribute specified as `"transcript_id"`. Defaults to `"ensembl_"`.
`columns`	a named character vector to list out the names and types of the other columns that the downloaded track should have. Use `UCSCFeatureDbTableSchema` to retrieve this information for a particular table.
`url,goldenPath_url`	use to specify the location of an alternate UCSC Genome Browser.
`chromCol`	If the schema comes back and the 'chrom' column has been labeled something other than 'chrom', use this argument to indicate what that column has been labeled as so we can properly designate it. This could happen (for example) with the knownGene track tables, which has no 'chromStart' or 'chromEnd' columns, but which DOES have columns that could reasonably substitute for these columns under particular circumstances. Therefore we allow these three columns to have arguments so that their definition can be re-specified
`chromStartCol`	Same thing as chromCol, but for renames of 'chromStart'
`chromEndCol`	Same thing as chromCol, but for renames of 'chromEnd'
`txdb`	A TxDb object that represents a handle to a transcript database. This object type is what is returned by `makeTxDbFromUCSC`, `makeTxDbFromUCSC` or `makeTxDb`
`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

makeTxDbPackageFromUCSC is a convenience function that calls both the makeTxDbFromUCSC and the makeTxDbPackage functions. The makeTxDbPackageFromBiomart follows a similar pattern and calls the makeTxDbFromBiomart and makeTxDbPackage functions. supportedMiRBaseBuildValues is a convenience function that will list all the possible values for the miRBaseBuild argument.

Value

A TxDb object.

Author(s)

M. Carlson

Examples

## First consider relevant helper/discovery functions:
## Display the list of tables supported by makeTxDbPackageFromUCSC():
supportedUCSCtables()

## Can also list all the possible values for the miRBaseBuild argument:
supportedMiRBaseBuildValues()

## Next are examples of actually building a package:
## Not run: 
## Makes a transcript package for Yeast from the ensGene table at UCSC:
makeTxDbPackageFromUCSC(version="0.01", 
                        maintainer="Some One <so@someplace.org>", 
                        author="Some One <so@someplace.com>",
                        genome="sacCer2", 
                        tablename="ensGene")

## Makes a transcript package from Human by using biomaRt and limited to a 
## small subset of the transcripts.
transcript_ids <- c(
    "ENST00000400839",
    "ENST00000400840",
    "ENST00000478783",
    "ENST00000435657",
    "ENST00000268655",
    "ENST00000313243",
    "ENST00000341724")
    
makeTxDbPackageFromBiomart(version="0.01", 
                           maintainer="Some One <so@someplace.org>", 
                           author="Some One <so@someplace.com>",
                           transcript_ids=transcript_ids)


## End(Not run)

[Package GenomicFeatures version 1.20.1 Index]