makeTxDbPackage {GenomicFeatures} | R Documentation |
The makeTxDbPackageFromUCSC
function allows the user
to make a TranscriptDb object 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
TranscriptDb object from transcript annotations that are in
a custom transcript Database, such as could be produced using
makeTranscriptDb
.
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, miRBaseBuild=NA) makeTxDbPackage(txdb, version, maintainer, author, destDir=".", license="Artistic-2.0") supportedMiRBaseBuildValues()
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
|
dataset |
which dataset from BioMart. For example:
|
genome |
genome abbreviation used by UCSC and obtained by
|
track |
name of the UCSC track. Use
|
tablename |
name of the UCSC table containing the transcript
annotations to retrieve. Use the |
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 TranscriptDb 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. |
columns |
a named character vector to list out the names and
types of the other columns that the downloaded track should
have. Use |
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 TranscriptDb object that represents a handle to a
transcript database. This object type is what is returned by
|
miRBaseBuild |
specify the string for the appropriate build
Information from mirbase.db to use for microRNAs. This can be
learned by calling |
makeTxDbPackageFromUCSC
is a convenience function that calls
both the makeTranscriptDbFromUCSC
and the
makeTxDbPackage
functions. The
makeTxDbPackageFromBiomart
follows a similar pattern and
calls the makeTranscriptDbFromBiomart
and
makeTxDbPackage
functions.
supportedMiRBaseBuildValues
is a convenience function that will
list all the possible values for the miRBaseBuild argument.
A TranscriptDb object.
M. Carlson
ucscGenomes
,
DEFAULT_CIRC_SEQS
,
makeTranscriptDbFromUCSC
,
makeTranscriptDbFromBiomart
,
makeTranscriptDb
supportedUCSCtables
getChromInfoFromUCSC
getChromInfoFromBiomart
## 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)