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)