makeTxDbPackage: 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", taxonomyId=NA, 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, taxonomyId=NA)
  makeTxDbPackageFromBiomart( version, maintainer, author, destDir=".", license="Artistic-2.0", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS, filter=NULL, id_prefix="ensembl_", host="www.ensembl.org", port=80, taxonomyId=NA, miRBaseBuild=NA)
  makeTxDbPackage(txdb, version, 		  maintainer, author, 	          destDir=".", license="Artistic-2.0", pkgname=NULL)
  supportedMiRBaseBuildValues()

Arguments

version

What is the version number for this package?

maintainer

Who is the package maintainer? (must include email to be valid). Should be a person object, or something coercible to one, like a string. May be omitted if the author argument is a person containing someone with the maintainer role.

author

Who is the creator of this package? Should be a person object, or something coercible to one, like a character vector of names. The maintainer argument will be merged into this list.

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.

filter

Additional filters to use in the BioMart query. Must be a named list. An example is filter=as.list(c(source="entrez"))

host

The host URL of the BioMart. Defaults to www.ensembl.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

taxonomyId

By default this value is NA and the organism provided (or inferred) will be used to look up the correct value for this. But you can use this argument to override that and 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.

pkgname

By default this value is NULL and does not need to be filled in (a package name will be generated for you). But if you override this value, then the package and it's object will be instead named after this value. Be aware that the standard rules for package names will apply, (so don't include spaces, underscores or dashes)

Value

TxDb object.

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.

Examples

Run this code

## 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)

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