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") makeTxDbPackageFromBiomart( version, maintainer, author, destDir=".", license="Artistic-2.0", biomart="ensembl", dataset="hsapiens_gene_ensembl", transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS) makeTxDbPackage(txdb, version, maintainer, author, destDir=".", license="Artistic-2.0")
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
|
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. |
url,goldenPath_url |
use to specify the location of an alternate UCSC Genome Browser. |
txdb |
A TranscriptDb object that represents a handle to a
transcript database. This object type is what is returned by
|
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.
A TranscriptDb object.
M. Carlson
ucscGenomes
,
DEFAULT_CIRC_SEQS
,
makeTranscriptDbFromUCSC
,
makeTranscriptDbFromBiomart
,
makeTranscriptDb
## Display the list of tables supported by makeTxDbPackageFromUCSC(): supportedUCSCtables() ## 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)