Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/makeTxDbPackage.R
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | makeTxDbPackageFromUCSC(
version=,
maintainer,
author,
destDir=".",
license="Artistic-2.0",
genome="hg19",
tablename="knownGene",
transcript_ids=NULL,
circ_seqs=NULL,
url="http://genome.ucsc.edu/cgi-bin/",
goldenPath.url=getOption("UCSC.goldenPath.url"),
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=getOption("UCSC.goldenPath.url"),
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=NULL,
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,
provider=NULL,
providerVersion=NULL)
supportedMiRBaseBuildValues()
makePackageName(txdb)
|
version |
What is the version number for this package? |
maintainer |
Who is the package maintainer? (must include email
to be valid). Should be a |
author |
Who is the creator of this package? Should be
a |
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 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 |
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
|
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 TxDb object that represents a handle to a
transcript database. This object type is what is returned by
|
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 |
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) |
provider |
If not given, a default is taken from the 'Data source' field of the metadata table. |
providerVersion |
If not given, a default is taken from one of 'UCSC table', 'BioMart version' or 'Data source' fields of the metadata table. |
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.
makePackageName
creates a package name from a TxDb object.
This function is also used by OrganismDbi.
A TxDb object.
M. Carlson
makeTxDbFromUCSC
,
makeTxDbFromBiomart
,
makeTxDb
,
ucscGenomes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | ## First consider relevant helper/discovery functions:
## Get the list of tables known to work with makeTxDbPackageFromUCSC():
supportedUCSCtables(genome="hg19")
## 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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